Gene targeting using replicating DNA molecules

ABSTRACT

The invention provides novel methods of gene targeting using replication in order to increase the efficiency of targeted genetic modification in an eukaryotic organism. Included are vectors, expression cassettes, and modified cells, plants and seeds.

TECHNICAL FIELD

The present invention relates generally to plant molecular biology.

SUMMARY OF THE INVENTION

The present invention provides novel methods and compositions forcarrying out gene targeting. The method uses homologous recombinationprocesses endogenous in the cells of all organisms. Any gene of anyorganism can be modified by the methods of the invention as long as thesequence of at least a portion of the gene is known, or a DNA clone isavailable.

The invention provides methods for increasing gene targeting frequenciescomprising introducing into a target cell a targeting vector comprisingan origin of replication and further comprising a target modifyingsequence which is compatible with a target site in the genome of thetarget cell. The target modifying sequence comprises the sequencemodifications to be introduced into the target site sequence. Areplicase is also provided in the target cell. Replication of thetargeting vector stimulates homologous recombination between thetargeting vector and the target site resulting in a gene targetingevent.

In another embodiment, the invention provides methods for increasinggene targeting frequencies comprising introducing into a target cell atargeting vector comprising a transposon comprising an origin ofreplication and further comprising a target modifying sequence which iscompatible with a target site in the genome of the target cell. Atransposase is provided in the target cell, wherein the transposase iscapable of excising the transposon to produce a replication-competenttargeting vector. A replicase is also provided in the target cell.Replication of the targeting vector stimulates homologous recombinationbetween the targeting vector and the target site resulting in a genetargeting event.

In another embodiment the invention provides methods for increasing genetargeting frequencies comprising introducing into a target cell atargeting vector comprising an origin of replication and furthercomprising a target modifying sequence which is compatible with a targetsite in the genome of the target cell, wherein the origin of replicationand the target modifying sequence are flanked by site-specificrecombination sites. A site-specific recombinase capable of excising thetargeting vector to produce a replication-competent targeting vector isprovided. A replicase is also provided in the target cell. Replicationof the targeting vector stimulates homologous recombination between thetargeting vector and the target site resulting in a gene targetingevent.

The invention also provides cells and organisms produced by the methods.These cells or organisms comprise a modified target polynucleotidesequence produced by a method of the invention. The invention furtherprovides progeny or seed produced by the modified cells or organisms,wherein the progeny or seed have inherited the gene targetedmodification. The invention also provides isolated nucleic acids such astargeting vectors.

The compositions used in the invention comprise nucleic acids, such astargeting vectors, and expression cassettes. The compositions furthercomprise donor organisms comprising an integrated targeting vector, andtarget organisms comprising modified target sequences, and the progenyof each.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

The term “isolated” refers to material, such as a nucleic acid or aprotein, which is: (1) substantially or essentially free from componentswhich normally accompany or interact with the material as found in itsnaturally occurring environment or (2) if the material is in its naturalenvironment, the material has been altered by deliberate humanintervention to a composition and/or placed at a locus in the cell otherthan the locus native to the material.

As used herein, “polypeptide” and “protein” are used interchangeably andmean proteins, protein fragments, modified proteins, amino acidsequences and synthetic amino acid sequences. The polypeptide can beglycosylated or not.

As used here, “polynucleotide” and “nucleic acid” are usedinterchangeably. A polynucleotide can be full-length or a fragment andincludes polynucleotides that have been modified for stability. Unlessotherwise indicated, the term includes reference to a specific sequenceor its complement.

As used herein, “functional variant” or “functional derivative” or“functional fragment” are used interchangeably. As applied topolypeptides, the functional variant or derivative is a fragment, amodified polypeptide, or a synthetic polypeptide that provides afunctional activity in a manner similar to the wild type, or naturallyoccurring, gene products

As used herein, “origin of replication” refers to a polynucleotideregion where DNA replication is initiated. The origin of replication isintended to include functional fragments, modifications, variants, andderivatives which retain the functional activity. Replication is usuallyinitiated at the origin of replication by a replicase polypeptide.

As used herein, “replicase”, or “replicase polypeptide” refers topolypeptides capable of stimulating DNA synthesis. The polynucleotidesand polypeptides are intended to include functional variants, fragments,and derivatives which retain the functional activity. The polypeptidesinclude proteins commonly referred to as “replication proteins”,“replication associated proteins”, or “replication initiation proteins”.The polypeptide includes proteins in which all the “replicationassociated” or “replication” functions are encoded as a single protein,and those in which these functions are carried out by more than oneprotein, irrespective of whether proper or “inappropriate” splicing hasoccurred prior to translation.

As used herein, “replicase polynucleotide” refers to polynucleotidescoding for a replicase polypeptide, including functional variants,derivatives, fragments, or functional homologs of characterizedreplicase polynucleotides. Replicase polynucleotides, functionalvariants and/or functional homologs from any organism can be used in themethods of the invention as long as the expressed replicase polypeptidesbind to the origin of replication, and/or stimulate DNA replication.

As used herein, “plant” includes but is not limited to whole plants,plant parts, plant cells, plant tissue, and plant seeds.

As used herein, “site-specific recombinase” refers to any enzyme capableof being functionally expressed that catalyzes conservativesite-specific recombination between its corresponding site-specificrecombination sites. The site-specific recombinase may be naturallyoccurring, or a recombinantly produced polypeptide, fragment, variant,or derivative thereof that retains the activity of the naturallyoccurring recombinase.

As used herein “gene targeting” refers to a process whereby a specificsequence modification is facilitated at a desired genetic locus by atransforming nucleic acid, such as a targeting vector. Typically, thegene at the target locus is modified, removed, replaced or duplicated bythe transforming nucleic acid. Modifications include at least oneinsertion, deletion, or substitution of one or more nucleotides at atarget site.

As used herein “homologous recombination” refers to the process by whicha recombination event occurs between two homologous nucleic acidregions.

As used herein “transposon” refers to a DNA sequence capable of movingfrom one place in the genome to another. Transposons are typicallycharacterized by being flanked by terminal inverted repeat sequencesrequired for transposition.

As used herein “transposase” refers to a polypeptide that mediatestransposition of a transposon from one location in the genome toanother. Transposases typically function to excise the transposon, andto recognize subterminal repeats and bring together the ends of theexcised transposon, in some systems other proteins are also required tobring together the ends during transposition.

As used herein “targeting vector” refers to a nucleic acid comprising atleast an origin of replication and a target modifying polynucleotide,wherein the target modifying polynucleotide comprises a modified versionof the target sequence, containing any sequence modification to beintroduced at the target site resulted in a desired genetic change atthe target. The targeting vector can be integrated in a host genome andlater excised to produce a gene targeting event. The targeting vectorcan be provided by any transformation method or introduced by sexualcrossing.

As used herein “target polynucleotide” or “target site” refers to apolynucleotide sequence to be modified in the host organism. The targetpolynucleotide can be either an endogenous polynucleotide, or anexogenous polynucleotide previously introduced into the host organism.The target sequence may be any polynucleotide sequence, including butnot limited to a polypeptide coding region. The target sequence may be anon-coding region, for example, a promoter, an intron, a terminator, anenhancer, or any other regulatory, structural polynucleotide, or otherpolynucleotide region.

As used herein “target modifying polynucleotide” refers to apolynucleotide comprising the sequence modification to be incorporatedat the target site, wherein the sequence modification comprises at leastone base pair difference as compared to the target site sequence.Sequence modifications to the target polynucleotide may includenucleotide substitutions, nucleotide or polynucleotide deletions, and/ornucleotide or polynucleotide insertions.

As used herein “donor organism” or “donor cell” refers to an organism,or cell, which comprises at least one of the following: a targetingvector, a replicase expression cassette, a recombinase expressioncassette, and/or a transposase expression cassette, such that thosecomponents contained can be delivered to a target host organism in aheritable manner. For example, the component(s) may be delivered bysexually crossing the target host to the donor organism.

As used herein “target organism”, “target cell”, “host organism”, or“host cell” refers to an organism, or cell, which comprises at least onetarget polynucleotide to be modified. Any one of the following: atargeting vector, a target modifying polynucleotide, a replicaseexpression cassette, a recombinase expression cassette, and/or atransposase expression cassette, may be introduced by any meansincluding transient or stable transformation, sexually crossing to adonor, or fusion to a donor cell.

As used herein “expression cassette” refers to a nucleic acid construct,generated recombinantly or synthetically, with a series of specifiednucleic acid elements which permit transcription of a particular nucleicacid in a host cell. The expression cassette can be incorporated into aplasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleicacid fragment. Typically, the expression cassette portion of anexpression vector includes, among other sequences, a nucleic acid to betranscribed, and a promoter.

As used herein “operably linked” includes reference to a functionallinkage between a promoter and a second sequence, wherein the promotersequence initiates and mediates transcription of the DNA sequencecorresponding to the second sequence. Generally, operably linked meansthat the nucleic acid sequences being linked are contiguous and, wherenecessary to join two protein coding regions, contiguous and in the samereading frame.

In general, the invention provides a method for gene targeting in anorganism by providing a targeting vector comprising a target modifyingpolynucleotide and an origin of replication, and providing replicaseactivity such that targeted sequence modifications are incorporated atthe target site in the host genome. The target site can be anypolynucleotide region, including but not limited to polypeptide codingregions, introns, exons, untranslated regions (UTR's), promoters,enhancers, terminators, or other regulators of gene expression, or anyother region of interest. The targeting vector comprises at least anorigin of replication and a target modifying polynucleotide. The targetmodifying polynucleotide shares sufficient homology with the target siteso that homologous recombination can occur between the twopolynucleotides. The target modifying polynucleotide has at least onebase pair difference as compared to the target site, this base pairdifference can comprise a point mutation (base change), insertion, ordeletion. When replicase activity is provided, the frequency ofincorporation of the sequence modifications at the target site isenhanced. The target site modification includes any changes which couldsuppress gene expression, such as the introduction of a premature stopcodon, frameshift mutation, or changes to a promoter or other UTR, andthe like. The changes also include modifications to increase geneexpression or protein activity such as alterations to codons, oralterations to UTR's and the like. The targeting vector need not beintegrated into the host genome, but may be maintained as anautonomously replicating vector. The targeting vector need not becircular in order to replicate, as illustrated by the work of Jeske etal. (2001) EMBO 20:6158–6167. The targeting vector may be introduced byany method, depending on the organism, including Agrobacterium-mediatedtransformation, biolistic methods, direct DNA delivery methods includingmicroinjection, chemical methods, electroporation and the like.

The targeting vector may further comprise a replicase expressioncassette wherein a replicase polynucleotide is operably linked to apromoter and other regulatory elements needed for expression of areplicase polypeptide. The promoter can be constitutive, inducible, orunder developmental control as needed in order to regulate theexpression of the replicase polypeptide.

If the targeting vector is incorporated into the genome, a method ofexcision can be used to release the targeting vector. The targetingvector may comprise flanking sequences for excision using systems suchas site-specific recombinases, or transposases. The recombinase ortransposase activity may be introduced using a recombinant expressioncassette wherein the recombinase or transposase is operably linked to apromoter and other regulatory elements needed for expression of thepolypeptide. The recombinase or transposase activity may also beprovided by crossing a donor organism, which comprises a recombinase ortransposase expression cassette, with a target organism comprising theintegrated targeting vector. Methods of providing the transposase bycrossing organisms are disclosed in WO 01/71019, the contents of whichare herein incorporated by reference.

Replication

Examples of replication systems suitable for this invention includebacterial origins of replication and replication proteins, viral originsof replication and replication proteins, and eukaryotic replicationsystems.

Examples of suitable viral replication systems include abutilon mosaicvirus (AbMV), African cassaya mosaic virus (ACMV), banana streak virus(BSV), bean dwarf mosaic virus (BDMV), bean golden mosaic virus (BGMV),beet curly top virus (BCTV), beet western yellow virus (BWYV), and otherluteoviruses, cassaya latent virus (CLV), carnation etched ring virus(CERV), cauliflower mosaic virus (CaMV), chloris striate mosaic virus(CSMV), commelina yellow mottle virus (CoYMV), cucumber mosaic virus(CMV), dahlia mosaic virus (DMV), digitaria streak virus (DSV), figwortmosaic virus (FMV), hop stunt viroid (HSV), maize streak virus (MSV),mirabilias mosaic virus (MMV), miscanthus streak virus (MiSV), potatostunt tuber virus (PSTV), panicum streak virus (PSV), potato yellowmosaic virus (PYMV), rice tungro bacilliform virus (RTBV), soybeanchlorotic mottle virus (SoyCMV), squash leaf curl virus (SqLCV),strawberry vein banding virus (SVBV), sugarcane streak virus (SSV),thistle mottle virus (ThMV), tobacco mosaic virus (TMV), tomato goldenmosaic virus (TGMV), tomato mottle virus (TmoV), tobacco ringspot virus(TobRV), tobacco yellow dwarf virus (TobYDV), tomato leaf curl virus(TLCV), tomato yellow leaf curl virus (TYLCV), tomato yellow leaf curlvirus—Thailand (TYLCV-t), wheat dwarf virus (WDV), and the bean yellowdwarf virus (BYDV). Other plant viruses with DNA replicases suitable foruse in the invention include members of the nanovirus group such asbanana bunchy top virus (BBTV), milk vetch dwarf virus (MDV),subterranean clover stunt virus (SCSV), and Ageratum yellow vein virus(AYVV).

Other virus systems include the papova viruses such as SV40, polyomaviruses, adenoviruses, papillomaviruses such as human papillomavirus(HPV) and bovine papillomavirus (BPV), herpes viruses such as herpessimplex virus (HSV), cytomegalovirus (CMV), and Epstein-Barr virus(EBV), and retroviruses such as human immunodeficiency virus (HIV),human T lymphotropic virus (HTVL), simian immunodeficiency virus (SIV),simian sarcoma virus (SSV), Rous sarcoma virus (RSV), caprinearthritis-encephalitis virus (CAEV), murine leukemia virus (MLV), avianleukemia virus (ALV), bovine leukemia virus (BLV), felineimmunodeficiency virus (FIV), equine infectious anemia virus (EIAV), andendogenous retrovirus (ERV), or a baculovirus system. For example, aviral vector system for use in animal cells is disclosed in WO 99/09139,and herein incorporated by reference.

Excision of Integrated Targeting Vectors

The targeting vector, flanked by site-specific recombination sitesand/or transposon sequences, may be randomly integrated in the genome ofa donor or target organism. Gene targeting can be activated by excisingthe target vector, which is then capable of replication and homologousrecombination with the target sequence. The integrated vector may beexcised by providing site-specific recombinase or a transposaseactivity. Any system or method to excise the integrated targeting vectorcan be used in the invention.

Examples of transposons and transposases suitable for this inventioninclude the P element transposon from Drosophila (Gloor, G. B. et al.(1991) Science 253:1110–1117), the Copia, Mariner and Minos elementsfrom Drosophila, the Hermes elements from the housefly, the PiggyBackelements from Trichplusia ni, Tc1 elements from C. elegans, the Ac/Ds,Dt/rdt, Mu-M1/Mn, and Spm(En)/dSpm elements from maize, the Tam elementsfrom snapdragon, the Mu transposon from bacteriophage, bacterialtransposons (Tn) and insertion sequences (IS), Ty elements of yeast(retrotransposon), Ta1 elements from Arabidopsis (retrotransposon), IAPelements from mice (retrotransposon), and the like. A transposableelement system effective in vertebrates and invertebrates is a syntheticSB transposon system derived from Tc1/mariner disclosed in WO 98/40510,the contents of which is herein incorporated by reference.

Site-specific recombination systems are reviewed in Sauer (1994) CurrentOpinion in Biotechnology 5:521–527, Nunes-Duby et al. (1998) Nucl. AcidsRes. 26:391–406, and Sadowski (1993) FASEB 7:760–767, the contents ofwhich are herein incorporated by reference. Any site-specificrecombination system can be used in the invention. Examples ofsite-specific recombination systems suitable for this invention includethe integrase family, such as the FLP/FRT system from yeast, and theCre/Lox system from bacteriophage P1, as well as the Int, and R systems.The resolvase family can also be used, for example γδ resolvase, and thelike. Examples of site-specific recombination systems used in plants canbe found in U.S. Pat. Nos. 5,929,301; 6,175,056; WO 99/25821; U.S. Pat.No. 6,331,661; WO 99/25855; WO 99/25841, and WO 99/25840, the contentsof each are herein incorporated by reference.

Markers

Gene targeting can be performed without selection if there is asensitive method for identifying recombinants, for example if thetargeted gene modification can be easily detected by PCR analysis, or ifit results in a certain phenotype. However, in most cases,identification of gene targeting events will be facilitated by the useof markers. Markers useful in the invention include positive andnegative selectable markers as well as markers that facilitatescreening, such as visual markers. Selectable markers include genescarrying resistance to an antibiotic such as spectinomycin (e.g. theaada gene, Svab et al. 1990 Plant Mol. Biol. 14:197), streptomycin(e.g., aada, or SPT, Svab et al. 1990 Plant Mol. Biol. 14:197; Jones etal. 1987 Mol. Gen. Genet 210:86), kanamycin (e.g., nptII, Fraley et al.1983 PNAS 80:4803), hygromycin (e.g., HPT, Vanden Elzen et al. 1985Plant Mol. Biol. 5:299), gentamycin (Hayford et al. 1988 Plant Physiol.86:1216), phleomycin, zeocin, or bleomycin (Hille et al. 1986 Plant Mol.Biol. 7:171), or resistance to a herbicide such as phosphinothricin (bargene), or sulfonylurea (acetolactate synthase (ALS)) (Charest et al.(1990) Plant Cell Rep. 8:643), genes that fulfill a growth requirementon an incomplete media such as HIS3, LEU2, URA3, LYS2, and TRP1 genes inyeast, and other such genes known in the art. Negative selectablemarkers include cytosine deaminase (codA) (Stougaard 1993 Plant J.3:755–761), tms2 (DePicker et al. 1988 Plant Cell Rep. 7:63–66), nitratereductase (Nussame et al. 1991 Plant J. 1:267–274), SU1 (O'Keefe et al.1994 Plant Physiol. 105:473–482), aux-2 from the Ti plasmid ofAgrobacterium, and thymidine kinase. Screenable markers includefluorescent proteins such as green fluorescent protein (GFP) (Chalfie etal., 1994 Science 263:802; U.S. Pat. Nos. 6,146,826; U.S. 5,491,084; andWO 97/41228), reporter enzymes such as β-glucuronidase (GUS) (JeffersonR. A. 1987 Plant Mol. Biol. Rep. 5:387; U.S. Pat. No. 5,599,670; andU.S. 5,432,081), β-galactosidase (lacZ), alkaline phosphatase (AP),glutathione S-transferase (GST) and luciferase (U.S. Pat. No. 5,674,713;and Ow et al. 1986 Science 234(4778):856–859), visual markers likeanthocyanins such as CRC (Ludwig et al. (1990) Science247(4841):449–450) R gene family (e.g. Lc, P, S), A, C, R-nj, bodyand/or eye color genes in Drosophila, coat color genes in mammaliansystems, and others known in the art.

One or more markers may be used in order to select and screen for genetargeting events. One common strategy for gene disruption involves usinga target modifying polynucleotide in which the target is disrupted by apromoterless selectable marker. Since the selectable marker lacks apromoter, random integration events are unlikely to lead totranscription of the gene. Gene targeting events will put the selectablemarker under control of the promoter for the target gene. Gene targetingevents are identified by selection for expression of the selectablemarker. Another common strategy utilizes a positive-negative selectionscheme. This scheme utilizes two selectable markers, one that confersresistance (R⁺) coupled with one that confers a sensitivity (S⁺), eachwith a promoter. When this polynucleotide is randomly inserted, theresulting phenotype is R⁺/S⁺. When a gene targeting event is generated,the two markers are uncoupled and the resulting phenotype is R⁺/S⁻.Examples of using positive-negative selection are found in Thykjær etal. (1997) Plant Mol. Biol. 35:523–530; and WO 01/66717, which areherein incorporated by reference.

Target Sequences

The methods of the invention can be practiced in any organism in which amethod of transformation is available, and for which there is at leastsome sequence information for the target sequence of interest, or for aregion flanking the target sequence of interest. It is also understoodthat two or more sequences could be targeted by sequentialtransformation, co-transformation with more than one targeting vector,or the construction of a targeting vector comprising more than onetarget modifying sequences.

The target sequences can be selected from any portion of a genome ofinterest. Typically, targets comprise genes or regulatory regions,although regions adjacent to or near genes may be selected such thatmodifications may be made without disrupting gene expression.

General categories of target sequences of interest include, for example,those genes involved in information, such as zinc fingers, thoseinvolved in communication, such as kinases, and those involved inhousekeeping, such as heat shock proteins.

Target sequences further include coding regions and non-coding regionssuch as promoters, enhancers, terminators, introns and the like, whichmay be modified in order to alter the expression of a gene of interest.For example, an intron sequence can be added to the 5′ region toincrease the amount of mature message that accumulates (see for exampleBuchman and Berg, Mol. Cell Biol. 8:4395–4405 (1988); and Callis et al.,Genes Dev. 1:1183–1200 (1987)).

The target sequence may be an endogenous sequence, or may be anintroduced exogenous sequence, or transgene. For example, this methodmay be used to alter the regulation or expression of a transgene, or toremove a transgene or other introduced sequence such as an introducedsite-specific recombination site. A sequence of interest could also beintroduced at a target site, for example a site-specific recombinationsite could be introduced, a endonuclease restriction site could beintroduced, a polynucleotide tag could be introduced, or a proteinpurification tag such as that encoding hexa-histidine could be insertedto facilitate purification of a expressed protein of interest.

In plants, more specific categories of target sequences include genesencoding agronomic traits, insect resistance, disease resistance,herbicide resistance, sterility, grain characteristics, and commercialproducts. Genes of interest also included those involved in oil, starch,carbohydrate, or nutrient metabolism as well as those affecting, forexample, kernel size, sucrose loading, and the like. The quality ofgrain is reflected in traits such as levels and types of oils, saturatedand unsaturated, quality and quantity of essential amino acids, andlevels of cellulose.

Herbicide resistance traits may include genes coding for resistance toherbicides that act to inhibit the action of acetolactate synthase(ALS), in particular the sulfonylurea-type herbicides (e.g., theacetolactate synthase (ALS) gene containing mutations leading to suchresistance, in particular the S4 and/or Hra mutations). Glyphosatetolerance can be obtained form the EPSPS gene.

Sterility genes can also be targeted, including male tissue-preferredgenes and genes with male sterility phenotypes such as QM, described inU.S. Pat. No. 5,583,210. Other genes include kinases and those encodingcompounds toxic to either male or female gametophytes.

For example, in Arabidopsis, the TGA3 locus was knocked out bydisrupting the gene with a kanamycin-resistance cassette (Maio and Lam(1995) Plant J. 7:359–365). The targeting cassette had about 4 kb ofhomology to the 5′ end of TGA3 and about 3 kb of homology to the 3′ endof the gene. In another report, the AGL5 MADS-box gene has been knockedout by homologous recombination in Arabidopsis (Kempin et al. 1997Nature 389:802–803). The targeting construct consisted of akanamycin-resistance cassette inserted into the AGL5 sequence roughly 3kb from the 5′ end and 2 kb from the 3′ end.

In animals, more specific categories of target sequences include genesinvolved in various diseases or medical conditions, such as cancer,including targets such as tumor suppressor genes (e.g., p53, p73, p51,or p40) and oncogenes (e.g., c-myc, c-jn, c-fos, c-rel, c-qin, c-neu,c-src, c-abl, c-lck, c-mil/raf, c-ras, c-sis, or c-fps); obesity,fertility, diabetes, hypertension, coronary disease, neurologicaldisorders, cystic fibrosis, multiple sclerosis, muscular dystrophy,genetic disorders, and the like.

Target Modifying Sequences, Homologous Recombination, and Gene Targeting

Homologous recombination is recombination occurring as a result ofinteraction between segments of genetic material that is homologous overa sufficient length of nucleotide sequence. Homologous recombination isan enzyme-catalyzed process that occurs in essentially all cell types.The reaction takes place when nucleotide strands of homologous sequenceare aligned in proximity to one another, and entails breakingphosphodiester bonds in the nucleotide strands and rejoining withneighboring homologous strands or with an homologous sequence on thesame strand. The breaking and rejoining can occur with precision, suchthat the sequence fidelity is retained.

The frequency of homologous recombination is influenced by a number offactors. Different organisms vary with respect to the amount ofhomologous recombination that occurs in their cells and the relativeproportion of homologous to non-homologous recombination that occurs isalso species-variable. Generally, the length of the region of homologyaffects the frequency of homologous recombination events, the longer theregion of homology, the greater the frequency. The length of thehomology region needed to observe homologous recombination is alsospecies-variable. In many cases, at least 5 kb of homology has beenutilized, but homologous recombination has been observed with as littleas 25–50 bp of homology. The minimum length of homology needed has beenestimated at 20–50 bp in E. coli (Singeret al. (1982) Cell 31:25–33;Shen & Huang (1986) Genetics 112:441–457; Watt et al. (1985) PNAS82:4768–4772), 63–89 bp in S. cerevisaie (Sugawara & Haber (1992) Mol.Cell. Biol. 12:563–575), and 163–300 bp in mammalian cells (Rubnitz &Subramani (1984) Mol. Cell. Biol. 4:2253–2258; Ayares et al. (1986) PNAS83:5199–5203; Liskay et al. (1987) Genetics 115:161–167).

However, differences in the frequency of homologous recombination can beoffset somewhat by sensitive selection for recombinations that do occur.Other factors, such as the degree of homology between the donor (targetmodifying polynucleotide) and target sequence will also influence thefrequency of homologous recombination events, as is well-understood inthe art. In ES cells, Te Riele et al. observed that use of targetingconstructs based on isogenic DNA resulted in a 20-fold increase intargeting efficiency (Te Riele et al. (1992) PNAS 89:5128–5132). Theyconcluded that base sequence divergence between non-isogenic DNA sourceswas the major influence on homologous recombination efficiency. Absolutelimits for the length of homology or the degree of homology cannot befixed, but depend on the number of events that can be generated,screened, and selected. All such factors are well known in the art, andcan be taken into account when using the invention for gene targeting inany given organism.

Gene targeting has been demonstrated in insects. In Drosophila, Dray andGloor found that as little as 3 kb of total template:target homologysufficed to copy a large non-homologous segment of DNA into the targetwith reasonable efficiency. (Genetics 147:689–699 1997). UsingFLP-mediated DNA integration at a target FRT in Drosophila, Golic (Golicet al. (1997) Nucl. Acids Res. 25:3665) showed integration wasapproximately 10-fold more efficient when the donor and target shared4.1 kb of homology compared to 1.1 kb of homology. Therefore, data fromDrosophila indicates that 2–4 kb of homology is sufficient for efficienttargeting, but there is some evidence that much less homology maysuffice, on the order of about 30 bp to about 100 bp (Nassif & Engels(1993) PNAS 90:1262–1266; Keeler & Gloor (1997) Mol. Cell Biol.17:627–634).

Gene targeting has been demonstrated in plants. The parameters for genetargeting in plants have primarily been investigated by rescuingintroduced truncated selectable marker genes. In these experiments, thehomologous DNA fragments for homologous recombination were typicallybetween 0.3 kb to 2 kb. Observed frequencies for homologousrecombination were on the order of 10⁻⁴–10⁻⁵. See, for example, Halfteret al. (1992) Mol. Gen. Genet. 231:186–193; Offringa et al. (1990) EMBO9:3077–3084; Offringa et al. (1993) PNAS 90:7346–7350; Paszkowski et al.(1988) EMBO 7:4021–4026; Hourda and Paszkowski (1994) Mol. Gen. Genet.243:106–111; and Risseeuw et al. (1995) Plant J. 7:109–119.

An endogenous, non-selectable gene was targeted in Arabidopsis . Thetargeting vector contained a region of about 7 kb homologous to thetarget gene and the targeting frequency was estimated to be at least3.9×10⁻⁴ (Maio and Lam (1995) Plant J. 7:359–365).

Using a positive-negative selection scheme and a targeting vectorcontaining up to 22.9 kb of sequence homologous to the target, Thykjærand co-workers detected gene targeting with a frequency less than5.3×10⁻⁵, despite the large flanking sequences available forrecombination (Thykjær et al. (1997) Plant Mol. Biol. 35:523–530). InArabidopsis, the AGL5 MADS-box gene was knocked out by homologousrecombination (Kempin et al. (1997) Nature 389:802–803) using atargeting construct consisting of a kanamycin-resistance cassetteinserted into the AGL5 sequence roughly 3 kb from the 5′ end and 2 kbfrom the 3′ end. Of the 750 kanamycin-resistant transgenic lines thatwere generated, one line contained the anticipated insertion.

Gene targeting has also been accomplished in other organisms. Forexample, at least 150–200 bp of homology was required for homologousrecombination in the parasitic protozoan Leishmania, in regions lessthan 1 kb, a decrease in the length had a linear effect on the targetingfrequency, and the targeting frequency plateaus at 1–2 kb of homology(Papadopoulou and Dumas (1997) Nucl. Acids Res. 25:4278–4286). In thefilamentous fungus Aspergillus nidulans, gene replacement has beenaccomplished with as little as 50 bp flanking homology (Chaveroche etal. (2000) Nucl. Acids Res. 28(22):e97). Targeted gene replacement hasalso been demonstrated in the ciliate Tetrahymena thermophila (Gaertiget al. (1994) Nucl. Acids Res. 22:5391–5398).

In mammals, gene targeting has been most successful in the mouse aspluripotent embryonic stem cell lines exists (ES) that can be grown inculture, transformed, selected and introduced into an embryonic stage ofa mouse embryo. Embryos bearing inserted transgenic ES cells develop asgenetically chimeric offspring. By interbreeding siblings, homozygousmice carrying the selected genes can be obtained. An overview of theprocess is provided in Watson et al. (1992) Recombinant DNA, 2^(nd) Ed.,Scientific American Books distributed by W H Freeman & Co.; Capecchi, MR (1989) Trends in Genetics 5:70–76; and Bronson, S K (1994) J. Biol.Chem. 269:27155–27158. Both homologous and non-homologous recombinationoccur in mammalian cells. While both processes occur with low frequency,non-homologous recombination occurs more frequently than homologousrecombination. ES cells are transfected with a DNA construct thatcombines a donor DNA having the modification to be introduced at thetarget site combined with flanking sequence homologous to the targetsite, and marker genes as needed for selection, as well as any otherdesired sequences. The donor construct need not be integrated into thegenome initially, but can recombine with the target site by homologousrecombination, or become integrated by non-homologous recombination.Since homologous recombination events are rare, dual selection can beused to select for gene targeted events and to select against randomintegration. The selections are conveniently carried out in vitro on EScells in culture. Other screening, such as PCR, can also be used toidentify desired events. In general, the frequency of homologousrecombination is increased as the length of the region of homology inthe donor is increased, with at least 5 kb of homology commonly used.However, homologous recombination has been observed with as little as25–50 bp of homology. It has been observed that small deletions orinsertions into the target site are introduced with higher frequencythan point mutations, but any desired modification can be obtained byappropriate design of donor vector, and selection and/or screeningmethods.

In an effort to create a mouse model system for cystic fibrosis Kolleret al. used a targeting construct to disrupt exon 10 of the CTFR gene(Koller et al. (1991) PNAS 88:10730–10734). The construct sharedhomology to 7.8 kb of the target, spanning exon 10, and replaced part ofthe exon with two neo genes which causes a premature stop codon. A genetargeting frequency of 4×10⁻⁴ was observed in ES cells.

In ES cells comprising two renin genes (Ren-1D and Ren-2) which shareabout 95% sequence identity at the genomic level, a targeting constructwith about 5.5 kb of homology across exons 2–5 of Ren-1D specificallyrecombined only with the target gene with a gene targeting frequency of5.29×10⁻³ (Miller et al. (1992) PNAS 89:5020–5024). It was estimatedthat the targeting frequency observed was enhanced about 2.7-fold by theinclusion of a negative selectable marker in the targeting construct.

In order to study the transcriptional control of type I collagen, thefirst intron of ColIA1 was targeted in mouse ES cells (Hormuzdi et al.(1998) Mol. Cell. Biol. 18:3368–3375). The targeting construct, whichshared about 13 kb of homology to the target, resulted in a 1.3 kbdeletion in intron 1. Even though there is a large deletion in the firstintron, the study showed the intron was still correctly spliced.

A point mutation in β-globin causes sickle cell disease. Using amouse-human hybrid cell line, BSM, which contains human chromosome 11,the sickle cell allele β^(S)-globin was corrected to the normalβ^(A)-globin allele (Shesley et al. (1991) PNAS 88:4294–4298). Thetargeting vector comprised 4.7 kb of homology to the β-globin gene, aswell as a selectable marker outside of the target gene, and resulted ina gene targeting frequency of at least 1×10⁻⁴.

Gene targeting in mammals other than mouse has been limited by the lackof stem cells capable of being transplanted to oocytes or developingembryos. However, McCreath, K J et al. (2000) Nature 405:1066–1069 havereported successful gene targeting in sheep by transformation andselection in primary embryo fibroblast cells. The targeted fibroblastnuclei were transferred to enucleated egg cells followed by implantationin the uterus of a host mother. The technique yields a homozygous,non-chimeric offspring, however the time available for targeting andselection is short.

The organisms which can be used in the invention include, but are notlimited to: insects, including Coleoptera, Diptera, such as Drosophila,Hemiptera, Homoptera, Hymenoptera, Lepidoptera, and Orthoptera; plants,including both monocotyledonous and dicotyledonous plants such as, butnot limited to, maize, rice, wheat, oats, barley, sorghum, millet,soybean and other legumes, canola, Brassica, alfalfa, sunflower,safflower, Arabidopsis, cotton, potato, tomato, tobacco and the like;animals including mice, rats, sheep, pigs, bovines, amphibians, such asXenopus, fish, such as zebrafish, birds; invertebrates such as C.elegans; fungi (Chaveroche et al. (2000) Nucl. Acids Res. 28(22):e97;DeLozane and Spudich (1987) Science 236:1086–1091); and protozoa such asciliates (Gaertig et al. (1994) Nucl. Acids Res. 22:5891–5398), and/orparasitic protozoa (Papadopoulou and Dumas (1997) Nucl. Acids Res.25:4278–4286), and the like.

The targeted event can be effected in the whole organism, or limited tocertain tissue or cell types or even particular subcellular organelles.For example, homologous recombination has been used to target foreigngenes into the plastid genome in tobacco (Zoubenko et al. (1994) Nucl.Acids Res. 22:3819–3824), and to correct a defective gene inhematopoietic progenitor cells (Hatada et al. (2000) PNAS97:13807–13811).

The amount of homology shared between the target and the targetmodifying polynucleotide can vary and includes unit integral values inthe ranges of about 1–20 bp, 20–50 bp, 50–100 bp, 75–150 bp, 100–250 bp,150–300 bp, 200–400 bp, 250–500 bp, 300–600 bp, 350–750 bp, 400–800 bp,450–900 bp, 500–1000 bp, 600–1250 bp, 700–1500 bp, 800–1750 bp, 900–2000bp, 1–2.5 kb, 1.5–3 kb, 2–4 kb, 2.5–5 kb, 3–6 kb, 3.5–7 kb, 4–8 kb, 5–10kb, or up to and including the total length of the target site. Theseranges include every integer within the range, for example, the range of1–20 bp includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, and 20 bp.

Nucleic Acids

Polynucleotides, including targeting vectors, target modifyingpolynucleotides, replicase polynucleotides, origins of replication,recombinase polynucleotides, transposon polynucleotides, transposasepolynucleotides, selectable markers, and any other polynucleotides ofinterest, useful in the present invention can be obtained using (a)standard recombinant methods, (b) synthetic techniques, or combinationsthereof. In general, examples of appropriate molecular biologicaltechniques and instructions are found in Sambrook et al., MolecularCloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory,Vols. 1–3 (1989), Methods in Enzymology, Vol. 152: Guide to MolecularCloning Techniques, Berger and Kimmel, Eds., San Diego: Academic Press,Inc. (1987), Current Protocols in Molecular Biology, Ausubel, et al.,Eds., Greene Publishing and Wiley-Interscience, New York (1995); PlantMolecular Biology: A Laboratory Manual, Clark, Ed., Springer-Verlag,Berlin (1997), all are herein incorporated by reference.

Polynucleotides and functional variants useful in the invention can beobtained using primers that selectively hybridize under stringentconditions. Primers are generally at least 12 bases in length and can beas high as 200 bases, but will generally be from 15 to 75, typicallyfrom 15 to 50. Functional fragments can be identified using a variety oftechniques such as restriction analysis, Southern analysis, primerextension analysis, and DNA sequence analysis.

Variants of the nucleic acids can be obtained, for example, byoligonucleotide-directed mutagenesis, linker-scanning mutagenesis,mutagenesis using the polymerase chain reaction, and the like. See, forexample, Ausubel, pages 8.0.3–8.5.9. Also, see generally, McPherson(ed.), DIRECTED MUTAGENESIS: A Practical approach, (IRL Press, 1991).Thus, the present invention also encompasses DNA molecules comprisingnucleotide sequences that have substantial sequence similarity with theinventive sequences. Conservatively modified variants are preferred.

Nucleic acids produced by sequence shuffling of useful polynucleotidescan also be used. Sequence shuffling is described in PCT publication No.96/19256. See also, Zhang, J.-H., et al. Proc. Natl. Acad. Sci. USA94:4504–4509 (1997).

Also useful are 5′ and/or 3′ UTR regions for modulation of translationof heterologous coding sequences. Positive sequence motifs includetranslational initiation consensus sequences (Kozak, Nucleic Acids Res.15:8125 (1987)) and the 7-methylguanosine cap structure (Drummond etal., Nucleic Acids Res. 13:7375 (1985)). Negative elements includestable intramolecular 5′ UTR stem-loop structures (Muesing et al., Cell48:691 (1987)) and AUG sequences or short reading frames 5′ of theappropriate AUG in the 5′ UTR (Kozak, supra, Rao et al., Mol. and Cell.Biol. 8:284 (1988)).

Further, the polypeptide-encoding segments of the polynucleotides can bemodified to alter codon usage. Codon usage in the coding regions of thepolynucleotides of the present invention can be analyzed statisticallyusing commercially available software packages such as “CodonPreference” available from the University of Wisconsin Genetics ComputerGroup (see Devereaux et al., Nucleic Acids Res. 12: 387–395 (1984)) orMacVector 4.1 (Eastman Kodak Co., New Haven, Conn.).

For example, the polynucleotides can be optimized for enhanced orsuppressed expression in the target organism. In the case of plants,see, for example, EPA0359472; WO91/16432; Perlak et al. (1991) Proc.Natl. Acad. Sci. USA 88:3324–3328; and Murray et al. (1989) NucleicAcids Res. 17:477–498, the disclosures of which are incorporated hereinby reference. In this manner, the genes can be synthesized utilizingspecies-preferred codons.

The nucleic acids may conveniently comprise a multi-cloning sitecomprising one or more endonuclease restriction sites inserted into thenucleic acid to aid in isolation of the polynucleotide. Also,translatable sequences may be inserted to aid in the isolation of thetranslated polynucleotide of the present invention. For example, ahexa-histidine marker sequence provides a convenient means to purify theproteins of the present invention.

The polynucleotides can be attached to a vector, adapter, promoter,transit peptide or linker for cloning and/or expression of apolynucleotide of the present invention. Additional sequences may beadded to such cloning and/or expression sequences to optimize theirfunction in cloning and/or expression, to aid in isolation of thepolynucleotide, or to improve the introduction of the polynucleotideinto a cell. Use of cloning vectors, expression vectors, adapters, andlinkers is well known and extensively described in the art. For adescription of such nucleic acids see, for example, Stratagene CloningSystems, Catalogs 1995, 1996, 1997 (La Jolla, Calif.); and, AmershamLife Sciences, Inc, Catalog '97 (Arlington Heights, Ill.).

The targeting vectors may comprise large regions of DNA with homology tothe target site. Examples of construction of targeting vectors withlarge fragments of DNA are found in Lalioti and Heath (2001) Nucl. AcidsRes. 29(3):e14; Akiyama et al. (2000) Nucl. Acids Res. 28(16):e77; andAngrand et al. (1999) Nucl. Acids Res. 27(17):e16.Transformation-associated recombination (TAR) cloning methods may alsobe used to isolate large regions of DNA. Examples of minimal homologyrequired and selection of clones are found in Noskov et al. (2001) Nucl.Acids Res. 29(6):e32 and Noskov et al. (2002) Nucl. Acids Res. 30(2):e8.

To construct genomic libraries, large segments of genomic DNA aregenerated by random fragmentation. Examples of appropriate molecularbiological techniques and instructions are found in Sambrook et al.,Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring HarborLaboratory, Vols. 1–3 (1989), Methods in Enzymology, Vol.152: Guide toMolecular Cloning Techniques, Berger and Kimmel, Eds., San Diego:Academic Press, Inc. (1987), Current Protocols in Molecular Biology,Ausubel et al., Eds., Greene Publishing and Wiley-Interscience, New York(1995); Plant Molecular Biology: A Laboratory Manual, Clark, Ed.,Springer-Verlag, Berlin (1997). Kits for construction of genomiclibraries are also commercially available.

The genomic library can be screened using a probe based upon thesequence of a nucleic acid used in the present invention. Those of skillin the art will appreciate that various degrees of stringency ofhybridization can be employed in the assay; and either the hybridizationor the wash medium can be stringent. The degree of stringency can becontrolled by temperature, ionic strength, pH and the presence of apartially denaturing solvent such as formamide.

Typically, stringent hybridization conditions will be those in which thesalt concentration is less than about 1.5 M Na ion, typically about 0.01to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and thetemperature is at least about 30° C. for short probes (e.g., 10 to 50nucleotides) and at least about 60° C. for long probes (e.g., greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide.

The hybridization can be conducted under low stringency conditions whichinclude hybridization with a buffer solution of 30% formamide, 1 M NaCl,1% SDS (sodium dodecyl sulfate) at 37° C., and a wash in 1× to 2×SSC(20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50° C. In another option,the hybridization can be conducted under moderate stringency conditionswhich include hybridization in 40% formamide, 1 M NaCl, 1% SDS at 37°C., and a wash in 0.5× to 1×SSC at 55° C. In yet another option, thehybridization can be conducted under high stringency conditions whichinclude hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., anda wash in 0.1×SSC at 60° C.

An extensive guide to the hybridization of nucleic acids is found inTijssen, Laboratory Techniques in Biochemistry and MolecularBiology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2“Overview of principles of hybridization and the strategy of nucleicacid probe assays”, Elsevier, New York (1993); and Current Protocols inMolecular Biology, Chapter 2, Ausubel et al., Eds., Greene Publishingand Wiley-Interscience, New York (1995). Often, cDNA libraries will benormalized to increase the representation of relatively rare cDNAs.

The nucleic acids can be amplified from nucleic acid samples usingamplification techniques. For instance, polymerase chain reaction (PCR)technology can be used to amplify the sequences of polynucleotides ofthe present invention and related genes directly from genomic DNA orlibraries. PCR and other in vitro amplification methods may also beuseful, for example, to clone nucleic acid sequences that code forproteins to be expressed, to make nucleic acids to use as probes fordetecting the presence of the desired mRNA in samples, for nucleic acidsequencing, or for other purposes.

Examples of techniques useful for in vitro amplification methods arefound in Berger, Sambrook, and Ausubel, as well as Mullis et al., U.S.Pat. No. 4,683,202 (1987); and, PCR Protocols A Guide to Methods andApplications, Innis et al., Eds., Academic Press Inc., San Diego, Calif.(1990). Commercially available kits for genomic PCR amplification areknown in the art. See, e.g., Advantage-GC Genomic PCR Kit (Clontech).The T4 gene 32 protein (Boehringer Mannheim) can be used to improveyield of long PCR products.

PCR-based screening methods have also been described. Wilfinger et al.describe a PCR-based method in which the longest cDNA is identified inthe first step so that incomplete clones can be eliminated from study.BioTechniques, 22(3):481–486 (1997).

The nucleic acids can also be prepared by direct chemical synthesis bymethods such as the phosphotriester method of Narang et al., Meth.Enzymol. 68:90–99 (1979); the phosphodiester method of Brown et al.,Meth. Enzymol. 68:109–151 (1979); the diethylphosphoramidite method ofBeaucage et al., Tetra. Lett 22:1859–1862 (1981); the solid phasephosphoramidite triester method described by Beaucage and Caruthers,Tetra. Letts. 22(20):1859–1862 (1981), e.g., using an automatedsynthesizer, e.g., as described in Needham-VanDevanter et al., NucleicAcids Res., 12:6159–6168 (1984); and, the solid support method of U.S.Pat. No. 4,458,066.

Expression cassettes comprising the isolated polynucleotide sequences ofinterest are also provided. An expression cassette will typicallycomprise a polynucleotide operably linked to transcriptional initiationregulatory sequences that will direct the transcription of thepolynucleotide in the intended host cell, such as tissues of atransformed plant.

The construction of expression cassettes that can be employed inconjunction with the present invention is well known to those of skillin the art in light of the present disclosure. See, e.g., Sambrook etal. (1989) Molecular Cloning: A Laboratory Manual Cold Spring Harbor,N.Y.; Gelvin et al. (1990) Plant Molecular Biology Manual; Prakash etal. eds. (1993) Plant Biotechnology: Commercial Prospects and Problems,Oxford & IBH Publishing Co., New Delhi, India; and Heslot et al. (1992)Molecular Biology and Genetic Engineering of Yeasts CRC Press, Inc.,USA; each incorporated herein in its entirety by reference.

For example, expression cassettes may include (1) a nucleic acid underthe transcriptional control of 5′ and 3′ regulatory sequences and (2) adominant selectable marker. Such plant expression cassettes may alsocontain, if desired, a promoter regulatory region (e.g., one conferringinducible, constitutive, environmentally- or developmentally-regulated,or cell- or tissue-specific/selective expression), a transcriptioninitiation start site, a ribosome binding site, an RNA processingsignal, a transcription termination site, and/or a polyadenylationsignal.

Constitutive, tissue-preferred or inducible promoters can be employed.Examples of constitutive promoters include the cauliflower mosaic virus(CaMV) 35S transcription initiation region, the 1′- or 2′-promoterderived from T-DNA of Agrobacterium tumefaciens, the ubiquitin 1promoter, the Smas promoter, the cinnamyl alcohol dehydrogenase promoter(U.S. Pat. No. 5,683,439), the Nos promoter, the pEmu promoter, therubisco promoter, the GRP1-8 promoter and other transcription initiationregions from various plant genes known to those of skill.

Examples of inducible promoters are the Adh1 promoter which is inducibleby hypoxia or cold stress, the Hsp70 promoter which is inducible by heatstress, the PPDK promoter and the pepcarboxylase promoter which are bothinducible by light. Also useful are promoters which are chemicallyinducible, such as the In2-2 promoter which is safener induced (U.S.Pat. No. 5,364,780), the ERE promoter which is estrogen induced, and theAxig1 promoter which is auxin induced and tapetum specific but alsoactive in callus (PCT US01/22169).

Examples of promoters under developmental control include promoters thatinitiate transcription preferentially in certain tissues, such asleaves, roots, fruit, seeds, or flowers. An exemplary promoter is theanther specific promoter 5126 (U.S. Pat. Nos. 5,689,049 and 5,689,051).Examples of seed-preferred promoters include, but are not limited to, 27kD gamma zein promoter and waxy promoter, Boronat, A. et al. (1986)Plant Sci. 47:95–102; Reina, M. et al. Nucl. Acids Res. 18(21):6426; andKloesgen, R. B. et al. (1986) Mol. Gen. Genet. 203:237–244. Promotersthat express in the embryo, pericarp, and endosperm are disclosed inU.S. Pat. No. 6,225,529 and PCT publication WO 00/12733. The disclosureseach of these are incorporated herein by reference in their entirety.

Either heterologous or non-heterologous (i.e., endogenous) promoters canbe employed to direct expression of the nucleic acids of the presentinvention. These promoters can also be used, for example, in expressioncassettes to drive expression of antisense nucleic acids to reduce,increase, or alter concentration and/or composition of the proteins ofthe present invention in a desired tissue.

If polypeptide expression is desired, it is generally desirable toinclude a polyadenylation region at the 3′-end of a polynucleotidecoding region. The polyadenylation region can be derived from thenatural gene, from a variety of other plant genes, or from T-DNA. The 3′end sequence to be added can be derived from, for example, the nopalinesynthase or octopine synthase genes, or alternatively from another plantgene, or even from any other eukaryotic gene.

An intron sequence can be added to the 5′ untranslated region or thecoding sequence of the partial coding sequence to increase the amount ofthe mature message that accumulates. See for example Buchman and Berg,Mol. Cell Biol. 8:4395–4405 (1988); Callis et al., Genes Dev.1:1183–1200 (1987). Use of maize introns Adh1-S intron 1, 2, and 6, theBronze-1 intron are known in the art. See generally, The Maize Handbook,Chapter 116, Freeling and Walbot, Eds., Springer, New York (1994).

The vector comprising the polynucleotide sequences useful in the presentinvention will typically comprise a marker gene that confers aselectable phenotype on plant cells. Usually, the selectable marker genewill encode antibiotic or herbicide resistance. Suitable genes includethose coding for resistance to the antibiotic spectinomycin orstreptomycin (e.g., the aada gene), the streptomycin phosphotransferase(SPT) gene coding for streptomycin resistance, the neomycinphosphotransferase (NPTII) gene encoding kanamycin or geneticinresistance, the hygromycin phosphotransferase (HPT) gene coding forhygromycin resistance.

Suitable genes coding for resistance to herbicides include those whichact to inhibit the action of acetolactate synthase (ALS), in particularthe sulfonylurea-type herbicides (e.g., the acetolactate synthase (ALS)gene containing mutations leading to such resistance in particular theS4 and/or Hra mutations), those which act to inhibit action of glutaminesynthase, such as phosphinothricin or basta (e.g., the bar gene), orother such genes known in the art. The bar gene encodes resistance tothe herbicide basta and the ALS gene encodes resistance to the herbicidechlorsulfuron.

Typical vectors useful for expression of nucleic acids in higher plantsare well known in the art and include vectors derived from thetumor-inducing (Ti) plasmid of Agrobacterium tumefaciens described byRogers et al., Meth. In Enzymol., 153:253–277 (1987). Exemplary A.tumefaciens vectors useful herein are plasmids pKYLX6 and pKYLX7 ofSchardl et al., Gene, 61:1–11 (1987) and Berger et al., Proc. Natl.Acad. Sci. U.S.A., 86:8402–8406 (1989). Another useful vector herein isplasmid pBI101.2 that is available from Clontech Laboratories, Inc.(Palo Alto, Calif.). A variety of plant viruses that can be employed asvectors are known in the art and include cauliflower mosaic virus(CaMV), geminivirus, brome mosaic virus, and tobacco mosaic virus.

Useful polynucleotides can be expressed in either sense or anti-senseorientation as desired. In plant cells, it has been shown that antisenseRNA inhibits gene expression by preventing the accumulation of mRNAwhich encodes the enzyme of interest, see, e.g., Sheehy et al., Proc.Nat'l. Acad. Sci. (USA) 85: 8805–8809 (1988); and Hiatt et al., U.S.Pat. No. 4,801,340.

Another method of suppression is sense suppression. For an example ofthe use of this method to modulate expression of endogenous genes see,Napoli et al., The Plant Cell 2: 279–289 (1990) and U.S. Pat. No.5,034,323. Another method of down-regulation of the protein involvesusing PEST sequences that provide a target for degradation of theprotein.

Catalytic RNA molecules or ribozymes can also be used to inhibitexpression of plant genes. The inclusion of ribozyme sequences withinantisense RNAs confers RNA-cleaving activity upon them, therebyincreasing the activity of the constructs. The design and use of targetRNA-specific ribozymes is described in Haseloff et al., Nature 334:585–591 (1988).

A variety of cross-linking agents, alkylating agents and radicalgenerating species as pendant groups on polynucleotides of the presentinvention can be used to bind, label, detect, and/or cleave nucleicacids. For example, Vlassov, V. V., et al., Nucleic Acids Res (1986)14:4065–4076, describe covalent bonding of a single-stranded DNAfragment with alkylating derivatives of nucleotides complementary totarget sequences. A report of similar work by the same group is that byKnorre, D. G., et al., Biochimie (1985) 67:785–789. Iverson and Dervanalso showed sequence-specific cleavage of single-stranded DNA mediatedby incorporation of a modified nucleotide which was capable ofactivating cleavage (J Am Chem Soc (1987) 109:1241–1243). Meyer, R. B.,et al., J Am Chem Soc (1989) 111:8517–8519, effect covalent crosslinkingto a target nucleotide using an alkylating agent complementary to thesingle-stranded target nucleotide sequence. A photoactivatedcrosslinking to single-stranded oligonucleotides mediated by psoralenwas disclosed by Lee, B. L., et al., Biochemistry (1988) 27:3197–3203.Use of crosslinking in triple-helix forming probes was also disclosed byHome et al., J Am Chem Soc (1990) 112:2435–2437. Use of N4,N4-ethanocytosine as an alkylating agent to crosslink to single-strandedoligonucleotides has also been described by Webb and Matteucci, J AmChem Soc (1986) 108:2764–2765; Nucleic Acids Res (1986) 14:7661–7674;Feteritz et al., J. Am. Chem. Soc. 113:4000 (1991). Various compounds tobind, detect, label, and/or cleave nucleic acids are known in the art.See, for example, U.S. Pat. Nos. 5,543,507; 5,672,593; 5,484,908;5,256,648; and, 5,681,941.

Proteins useful in the present invention include proteins derived fromthe native protein by deletion (so-called truncation), addition orsubstitution of one or more amino acids at one or more sites in thenative protein. In constructing variants of the proteins of interest,modifications will be made such that variants continue to possess thedesired activity.

For example, amino acid sequence variants of the polypeptide can beprepared by mutations in the cloned DNA sequence encoding the nativeprotein of interest. Methods for mutagenesis and nucleotide sequencealterations are well known in the art. See, for example, Walker andGaastra, eds. (1983) Techniques in Molecular Biology (MacMillanPublishing Company, New York); Kunkel (1985) Proc. Natl. Acad. Sci. USA82:488–492; Kunkel et al. (1987) Methods Enzymol. 154:367–382; Sambrooket al. (1989) Molecular Cloning: A Laboratory Manual (Cold SpringHarbor, N.Y.); U.S. Pat. No. 4,873,192; and the references citedtherein; herein incorporated by reference. Guidance as to appropriateamino acid substitutions that do not affect biological activity of theprotein of interest may be found in the model of Dayhoff et al. (1978)Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found.,Washington, D.C.), herein incorporated by reference. Conservativesubstitutions, such as exchanging one amino acid with another havingsimilar properties, may be preferred.

The present invention includes catalytically active polypeptides (i.e.,enzymes). Catalytically active polypeptides will generally have aspecific activity of at least 20%, 30%, or 40%, or at least 50%, 60%, or70%, or at least 80%, 90%, 95%, or 100% that of the native(non-synthetic), endogenous polypeptide. Further, the substratespecificity (k_(cat)/K_(m)) is optionally substantially similar to thenative (non-synthetic), endogenous polypeptide. Typically, the K_(m)will be at least 30%, 40%, or 50%, that of the native (non-synthetic),endogenous polypeptide; or at least 60%, 70%, 80%, 90%, 95% or 100%.Methods of assaying and quantifying measures of enzymatic activity andsubstrate specificity (k_(cat)/K_(m)), are well known to those of skillin the art.

The methods of the present invention can be used with any cell such asbacteria, yeast, insect, mammalian, or plant cells. The transformedcells produce viral replicase protein.

An intermediate host cell may be used in the practice of this inventionto increase the copy number of the targeting vector, and/or replicase,recombinase, or transposase expression cassettes. With an increased copynumber, the vector containing the nucleic acid of interest can beisolated in significant quantities for introduction into the desiredtarget host cells. Intermediate host cells that can be used in thepractice of this invention include prokaryotes, including bacterialhosts such as Escherichia coli, Salmonella typhimurium, and Serratiamarcescens. Eukaryotic hosts such as yeast or filamentous fungi may alsobe used in this invention. One can use target host specific promotersthat do not cause expression of the polypeptide in bacteria.

Commonly used prokaryotic control sequences include promoters such asthe beta lactamase (penicillinase) and lactose (lac) promoter systems(Chang et al., Nature 198:1056 (1977)), the tryptophan (trp) promotersystem (Goeddel et al., Nucl. Acids Res. 8:4057 (1980)) and the lambdaderived P L promoter and N-gene ribosome binding site (Shimatake et al.,Nature 292:128 (1981)). The inclusion of selection markers in DNAvectors transfected in E. coli is also useful. Examples of such markersinclude genes specifying resistance to ampicillin, tetracycline, orchloramphenicol.

The vector is selected to allow introduction into the appropriate hostcell. Bacterial vectors are typically of plasmid or phage origin.Expression systems for expressing a protein of the present invention areavailable using Bacillus sp. and Salmonella (Palva et al. (1983) Gene22: 229–235; Mosbach et al. (1983) Nature 302: 543–545).

Synthesis of heterologous proteins in yeast is well known. See Sherman,F. et al. Methods in Yeast Genetics, Cold Spring Harbor Laboratory(1982). Two widely utilized yeast for production of eukaryotic proteinsare Saccharomyces cerevisiae and Pichia pastoris. Vectors, strains, andprotocols for expression in Saccharomyces and Pichia are known in theart and available from commercial suppliers (e.g., Invitrogen). Suitablevectors usually have expression control sequences, such as promoters,including 3-phosphoglycerate kinase or alcohol oxidase, and an origin ofreplication, termination sequences and the like as desired.

The protein can be isolated from yeast by lysing the cells and applyingstandard protein isolation techniques to the lysates. The monitoring ofthe purification process can be accomplished by using Western blottechniques or radioimmunoassay of other standard immunoassay techniques.

The proteins useful in the present invention can also be constructedusing non-cellular synthetic methods. Techniques for solid phasesynthesis are described by Barany and Merrifield, Solid-Phase PeptideSynthesis, pp. 3–284 in The Peptides: Analysis, Synthesis, Biology. Vol.2: Special Methods in Peptide Synthesis, Part A.; Merrifield et al., J.Am. Chem. Soc. 85:2149–2156 (1963), and Stewartet al., Solid PhasePeptide Synthesis, 2nd ed., Pierce Chem. Co., Rockford, III. (1984).Proteins of greater length may be synthesized by condensation of theamino and carboxy termini of shorter fragments. Methods of formingpeptide bonds by activation of a carboxy terminal end (e.g., by the useof the coupling reagent N,N′-dicyclohexylcarbodiimide) are known tothose of skill.

The proteins useful in this invention may be purified to substantialpurity by standard techniques well known in the art, including detergentsolubilization, selective precipitation with such substances as ammoniumsulfate, column chromatography, immunopurification methods, and others.See, for instance, R. Scopes, Protein Purification: Principles andPractice, Springer-Verlag: New York (1982); Deutscher, Guide to ProteinPurification, Academic Press (1990). For example, antibodies may beraised to the proteins as described herein. Purification from E. colican be achieved following procedures described in U.S. Pat. No.4,511,503. Detection of the expressed protein is achieved by methodsknown in the art, for example, radioimmunoassays, Western blottingtechniques or immunoprecipitation.

In certain embodiments, the invention can be practiced in a wide rangeof plants such as monocots and dicots. For example, the methods of thepresent invention can be employed in corn, soybean, sunflower,safflower, potato, tomato, sorghum, canola, wheat, alfalfa, cotton,rice, barley and millet.

Transformation

The method of transformation/transfection is not critical to theinvention; various methods of transformation or transfection arecurrently available. As newer methods are available to transform hostcells they may be directly applied. Accordingly, a wide variety ofmethods have been developed to insert a DNA sequence into the genome ofa host cell to obtain the transcription and/or translation of thesequence to effect phenotypic changes in the organism. Thus, any methodthat provides for efficient transformation/transfection may be employed.

A DNA sequence coding for the desired polynucleotide useful in thepresent invention, for example a cDNA, RNA or a genomic sequence, willbe used to construct an expression cassette that can be introduced intothe desired host. Isolated nucleic acid acids of the present inventioncan be introduced according techniques known in the art. Generally,expression cassettes as described above and suitable for transformationof are prepared.

For single-celled organisms and organisms that can be regenerated fromsingle cells, transformation can be carried out by in vitro culture,followed by selection for transformation and regeneration oftransformants. Methods often used for transferring DNA or RNA into cellsinclude microinjection, particle gun bombardment, forming DNA or RNAcomplexes with cationic lipids, liposomes or other carrier materials,electroporation, chemical methods, and viral methods. Other techniquesare known in the art, for example see standard reference works such asMethods in Enzymology, Methods in Cell Biology, Molecular BiologyTechniques, all published by Academic Press, Inc. NY. Methods fortransforming various host cells are disclosed in Klein et al.“Transformation of microbes, plants and animals by particlebombardment”, Bio/Technol. New York, N.Y., Nature Publishing Company,March 1992, 10(3):286–291. Waters has recently demonstrated the stabletransfer of nucleic acids from bacteria to cultured mammalian cells,apparently via cell conjugation (Waters, VL 2001 Nature Genetics29:375–376).

Transfer of the polynucleotide into the cell nucleus occurs by cellularprocesses and can sometimes be aided by choice of an appropriate vector,by including integration site sequences which can be acted upon by anintracellular transposase or recombinase. For reviews of transposase orrecombinase mediated integration see, e.g., Craig, NLK (1988) Ann RevGenet 22:77; Cox, MM (1988) In Genetic Recombination (Kucherlapati andSmith, Eds.) pp. 429–443, American Society for Microbiology, Washington,D.C.; Hoess, R H et al. (1990) In Nucleic Acid and Molecular Biology(Eckstein and Lilley, Eds.) Vol 4, pp. 99–109, Springer-Verlag, Berlin.

Direct transformation of multicellular organisms can often beaccomplished at an embryonic stage of the organism. For example, inDrosophila, as well as other insects, DNA can be microinjected into theembryo at a multinucleate stage where it can become integrated into manynuclei, some of which become the nuclei of germ line cells. Recently,stable germline transformations were reported in mosquito (Catteruccia,F., et al. (2000) Nature 405:954–962). By incorporating a marker as acomponent of the transforming DNA, non-chimeric progeny of the originaltransformant can be identified and maintained. Direct microinjectioninto egg or embryo cells has also been employed effectively fortransforming many species, Xenopus for example. In the mouse, theexistence of pluripotent embryonic stem (ES) cells that are amenable toculture in vitro has been used to generate transformed mice. The EScells can be transformed in culture, then microinjected into mouseblastocysts, where they integrate into the developing embryo andgenerate germline chimeras. By interbreeding heterozygous siblings,homozygous animals carrying the desired gene can be obtained. Forreviews of the methods for transforming multicellular organisms see,e.g. Haren et al. (1999) Ann Rev Microbiol 53:245–281; Reznikoff et al.(1999) Biochem Biophys Res Comm 266(3):729–734; Ivics et al. (1999)Methods in Cell Biology 60:99–131; Weinberg, E S (1998) Curr Biol8(7):R244–247; Hall et al. (1997) FEMS Microbiol Rev 21(2):157–178;Craig (1997) Ann Rev Biochem 66:437–474; Beall et al. (1997) Genes Dev11(16):2137–2151.

Techniques for transforming a wide variety of higher plant species arewell known and described in the technical, scientific, and patentliterature. See, for example, Weising et al., Ann. Rev. Genet 22:421–477 (1988). For example, the DNA construct may be introduceddirectly into the genomic DNA of the plant cell using techniques such aselectroporation, PEG-mediated transfection, particle bombardment,silicon fiber delivery, or microinjection of plant cell protoplasts orembryogenic callus. See, e.g., Tomes, et al., Direct DNA Transfer intoIntact Plant Cells Via Microprojectile Bombardment. pp. 197–213 in PlantCell, Tissue and Organ Culture, Fundamental Methods. eds. O. L. Gamborgand G. C. Phillips. Springer-Verlag Berlin Heidelberg New York, 1995.Alternatively, the DNA constructs may be combined with suitable T-DNAflanking regions and introduced into a conventional Agrobacteriumtumefaciens host vector. The virulence functions of the Agrobacteriumtumefaciens host will direct the insertion of the construct and adjacentmarker into the plant cell DNA when the cell is infected by thebacteria. See, U.S. Pat. No. 5,591,616.

The introduction of DNA constructs using polyethylene glycolprecipitation is described in Paszkowski et al., Embo J. 3: 2717–2722(1984). Electroporation techniques are described in Fromm et al., Proc.Natl. Acad. Sci. 82:5824 (1985). Ballistic transformation techniques aredescribed in Klein et al., Nature 327:70–73 (1987).

Agrobacterium tumefaciens-meditated transformation techniques are welldescribed in the scientific literature. See, for example Horsch et al.,Science 233: 496–498 (1984), and Fraley et al., Proc. Natl. Acad. Sci.80: 4803 (1983). For instance, Agrobacterium transformation of maize isdescribed in U.S. Pat. No. 5,550,318.

Other methods of transformation include (1) Agrobacteriumrhizogenes-mediated transformation (see, e.g., Lichtenstein and FullerIn: Genetic Engineering, vol. 6, P W J Rigby, Ed., London, AcademicPress, 1987; and Lichtenstein, C. P., and Draper, J. In: DNA Cloning,Vol. II, D. M. Glover, Ed., Oxford, IRI Press, 1985), ApplicationPCT/US87/02512 (WO 88/02405 published Apr. 7, 1988) describes the use ofA. rhizogenes strain A4 and its Ri plasmid along with A. tumefaciensvectors pARC8 or pARC16 (2) liposome-mediated DNA uptake (see, e.g.,Freeman et al., Plant Cell Physiol. 25:1353, 1984), (3) the vortexingmethod (see, e.g., Kindle, Proc. Natl. Acad. Sci., USA 87:1228, (1990).

DNA can also be introduced into plants by direct DNA transfer intopollen as described by Zhou et al., Methods in Enzymology, 101:433(1983); D. Hess, Intern Rev. Cytol., 107:367 (1987); Luo et al., PlantMol. Biol. Reporter, 6:165 (1988). Expression of polypeptide codingnucleic acids can be obtained by injection of the DNA into reproductiveorgans of a plant as described by Pena et al., Nature, 325:274 (1987).DNA can also be injected directly into the cells of immature embryos andthe rehydration of desiccated embryos as described by Neuhaus et al.,Theor. Appl. Genet., 75:30 (1987); and Benbrook et al., in ProceedingsBio Expo 1986, Butterworth, Stoneham, Mass., pp. 27–54 (1986).

Animal and lower eukaryotic (e.g., yeast) host cells are competent orrendered competent for transfection by various means. There are severalwell-known methods of introducing DNA into animal cells. These include:calcium phosphate precipitation, fusion of the recipient cells withbacterial protoplasts containing the DNA, treatment of the recipientcells with liposomes containing the DNA, DEAE dextran, electroporation,biolistics, and micro-injection of the DNA directly into the cells. Thetransfected cells are cultured by means well known in the art. Kuchler,R. J., Biochemical Methods in Cell Culture and Virology, Dowden,Hutchinson and Ross, Inc. (1977).

Transformed plant cells which are derived by any of the abovetransformation techniques can be cultured to regenerate a whole plantwhich possesses the transformed genotype. Such regeneration techniquesoften rely on manipulation of certain phytohormones in a tissue culturegrowth medium, typically relying on a biocide and/or herbicide markerwhich has been introduced together with a polynucleotide of the presentinvention. For transformation and regeneration of maize see, Gordon-Kammet al., The Plant Cell, 2:603–618 (1990).

Plants cells transformed with a plant expression vector can beregenerated, e.g., from single cells, callus tissue or leaf discsaccording to standard plant tissue culture techniques. It is well knownin the art that various cells, tissues, and organs from almost any plantcan be successfully cultured to regenerate an entire plant. Plantregeneration from cultured protoplasts is described in Evans et al.,Protoplasts Isolation and Culture, Handbook of Plant Cell Culture,Macmillan Publishing Company, New York, pp. 124–176 (1983); and Binding,Regeneration of Plants, Plant Protoplasts, CRC Press, Boca Raton, pp.21–73 (1985).

The regeneration of plants containing the foreign gene introduced byAgrobacterium can be achieved as described by Horsch et al., Science,227:1229–1231 (1985) and Fraley et al., Proc. Natl. Acad. Sci. U.S.A.,80:4803 (1983). This procedure typically produces shoots within two tofour weeks and these transformant shoots are then transferred to anappropriate root-inducing medium containing the selective agent and anantibiotic to prevent bacterial growth. Transgenic plants of the presentinvention may be fertile or sterile.

Regeneration can also be obtained from plant callus, explants, organs,or parts thereof. Such regeneration techniques are described generallyin Klee et al., Ann. Rev. of Plant Phys. 38: 467–486 (1987). Theregeneration of plants from either single plant protoplasts or variousexplants is well known in the art. See, for example, Methods for PlantMolecular Biology, A. Weissbach and H. Weissbach, eds., Academic Press,Inc., San Diego, Calif. (1988). For maize cell culture and regenerationsee generally, The Maize Handbook, Freeling and Walbot, Eds., Springer,N.Y. (1994); Corn and Corn Improvement, 3rd edition, Sprague and DudleyEds., American Society of Agronomy, Madison, Wis. (1988).

In vegetatively propagated crops, mature transgenic plants can bepropagated by the taking of cuttings or by tissue culture techniques toproduce multiple identical plants. Selection of desirable transgenics ismade and new varieties are obtained and propagated vegetatively forcommercial use. In seed propagated crops, mature transgenic plants canbe self crossed to produce a homozygous inbred plant. The inbred plantproduces seed containing the newly introduced heterologous nucleic acid.These seeds can be grown to produce plants that would produce theselected phenotype.

Parts obtained from the regenerated plant, such as flowers, seeds,leaves, branches, fruit, and the like are included in the invention,provided that these parts comprise cells comprising the isolatedpolynucleotide of interest. Progeny and variants, and mutants of theregenerated plants are also included within the scope of the invention,provided that these parts comprise the introduced nucleic acidsequences.

Transgenic plants expressing a selectable marker can be screened fortransmission of the polynucleotide of interest, for example, standardDNA detection techniques to detect the polynucleotide, and/orimmunoblots to detect protein expression. Transgenic lines are alsotypically evaluated on levels of expression of the heterologous nucleicacid. Expression at the RNA level can be determined initially toidentify and quantitate expression-positive plants. Standard techniquesfor RNA analysis can be employed and include PCR amplification assaysusing oligonucleotide primers designed to amplify only the heterologousRNA templates and solution hybridization assays using heterologousnucleic acid-specific probes. The RNA-positive plants can then analyzedfor protein expression by Western immunoblot analysis using thespecifically reactive antibodies of the present invention. In addition,in situ hybridization and immunocytochemistry according to standardprotocols can be done using heterologous nucleic acid specificpolynucleotide probes and antibodies, respectively, to localize sites ofexpression within transgenic tissue. Generally, a number of transgeniclines are usually screened for the incorporated nucleic acid to identifyand select plants with the most appropriate expression profiles.

Plants that can be used in the method of the invention vary broadly andinclude monocotyledonous and dicotyledonous plants including corn,soybean, sunflower, sorghum, canola, wheat, alfalfa, cotton, rice,barley, potato, tomato, and millet.

Seeds derived from plants regenerated from transformed plant cells,plant parts or plant tissues, or progeny derived from the regeneratedtransformed plants, may be used directly as feed or food, or furtherprocessing may occur.

One of skill will recognize that after the expression cassette is stablyincorporated in transgenic plants and confirmed to be operable, it canbe introduced into other plants by sexual crossing. Any of a number ofstandard breeding techniques can be used, depending upon the species tobe crossed. Further, one of skill will recognize that any component ofthe method can be introduced to the host organism by sexually crossingthe target host with a donor organism which comprises one of more of thefollowing: a targeting vector, and/or a replicase expression cassette, asite-specific recombinase expression cassette, or a transposaseexpression cassette. In the case of cells in culture, the components mayalso be brought together by fusing target cells and donor cells.

Any method described above in reference to plants can be applied to thegeneration and identification of gene targeting events in other targethost organisms. Examples of organisms which can be used in the inventioninclude, but are not limited to: insects, including Coleoptera, Diptera,such as Drosophila, Hemiptera, Homoptera, Hymenoptera, Lepidoptera, andOrthoptera; plants, including both monocotyledonous and dicotyledonousplants such as, but not limited to, maize, rice, wheat, oats, barley,sorghum, millet, soybean and other legumes, canola, Brassica, alfalfa,sunflower, safflower, Arabidopsis, cotton, potato, tomato, tobacco andthe like; animals including mice, rats, sheep, pigs, bovines,amphibians, such as Xenopus, fish, such as zebrafish, birds; andprotozoa such as ciliates, and/or parasitic protozoa, and the like.

Identification and Characterization of Modified Target Cells andOrganisms

Gene targeting can be performed without selection, if there is asensitive method for identifying recombinants, for example if thetargeted gene modification can be easily detected by PCR analysis, or ifit results in a certain phenotype. However, in most cases,identification of gene targeting events will be facilitated by the useof markers. Markers useful in the invention include positive andnegative selectable markers as well as markers that facilitatescreening, such as visual markers. Selectable markers include genescarrying resistance to an antibiotic such as spectinomycin (e.g. theaada gene), streptomycin (e.g., aada, or SPT), kanamycin (e.g., nptll),hygromycin (e.g., HPT), gentamycin, phleomycin, zeocin, or bleomycin, orresistance to a herbicide such as phosphinothricin (bar gene), orsulfonylurea (acetolactate synthase—ALS), genes that fulfill a growthrequirement on an incomplete media such as HIS3, LEU2, URA3, LYS2, andTRP1 genes in yeast, and other such genes known in the art. Negativeselectable markers include cytosine deaminase (codA) (Stougaard 1993Plant J. 3:755–761), tms2 (DePicker et al. 1988 Plant Cell Rep.7:63–66), nitrate reductase (Nussame et al. 1991 Plant J. 1:267–274),and SU1 (O'Keefe et al. 1994 Plant Physiol. 105:473–482). Screenablemarkers include fluorescent proteins such as green fluorescent protein(GFP) (Chalfie et al., 1994 Science 263:802; U.S. Pat. Nos. 6,146,826;U.S. 5,491,084; and WO 97/41228), reporter enzymes such asβ-glucuronidase (GUS) (Jefferson R. A. 1987 Plant Mol. Biol. Rep. 5:387;U.S. Pat. Nos. 5,599,670; and U.S. 5,432,081), β-galactosidase (lacZ),alkaline phosphatase (AP), glutathione S-transferase (GST) andluciferase (U.S. Pat. No. 5,674,713; and Ow et al. 1986 Science234(4778):856–859), visual markers such as color markers likeanthocyanins such as CRC (Ludwig et al. 1990 Science 247(4841):449–450)R gene family (e.g. Lc, P, S), A, C, R-nj, body and/or eye color genesin Drosophila, and coat color genes in mammalian systems, and othersknown in the art.

One or more markers may be used in order to select and screen for genetargeting events. One common strategy for gene disruption involves usinga target modifying polynucleotide in which the target is disrupted by apromoterless selectable marker. Since the selectable marker lacks apromoter, random integration events are unlikely to lead totranscription of the gene. Gene targeting events will put the selectablemarker under control of the promoter for the target gene. Gene targetingevents are identified by selection for expression of the selectablemarker. Another common strategy utilizes a positive-negative selectionscheme. This scheme utilizes two selectable markers, one that confersresistance (R⁺) coupled with one that confers a sensitivity (S⁺), eachwith a promoter. When this polynucleotide is randomly inserted, theresulting phenotype is R⁺/S⁺. When a gene targeting event is generated,the two markers are uncoupled and the resulting phenotype is R⁺/S⁻.Examples of using positive-negative selection are found in Thykjær etal. (1997) Plant Mol Biol. 35:523–530; and WO 01/66717, which are hereinincorporated by reference.

Cells or organisms identified by one or more selective markers can befurther screened for modification of the target polynucleotide ofinterest by a large number of molecular and biochemical assays known inthe art. For example, standard DNA detection techniques to detect thepolynucleotide including amplification techniques such as restrictionenzyme analysis, PCR, Southern and Northern blots, DNA chips, in situhybridization, sequencing and the like. PCR is fast, specific andsensitive method commonly used to detect gene targeting events. Primersthat distinguish between unmodified and modified target are designed andamplification conditions identified as known to those of skill in theart, see for example standard references such as Sambrook et al. (1989)Molecular Cloning, A Laboratory Manual 2^(nd) Ed. Cold Spring HarborPress New York, Walker and Gaastra, eds. (1983) Techniques in MolecularBiology, MacMillan Publishing New York, Innis et al. eds. (1990) PCRProtocols: A Guide to Methods and Applications, Academic Press, Inc. SanDiego, Calif., Ausubel et al., eds. (1995) Current Protocols inMolecular Biology, Greene Publishing and Wiley-Interscience, New York.See also, Kim and Smithies (1988) Nucl. Acids Res. 16:8887–8903.Biochemical and/or immunochemical assay to detect and/or quantifyprotein expression may also be employed, such as immunoblots,immunoprecipitation, ELISA assays, immunohistochemistry, enzyme activityassays, enzyme kinetic studies, chromatographic and electrophoreticseparations such as polyacrylamide gel profiles, capillaryelectrophoresis, protein binding/interaction assays such as ligandbinding, gel shift assays, blot overlays, co-immunoprecipitation, andthe like. Standard techniques for RNA analysis can be employed andinclude PCR amplification assays using oligonucleotide primers designedto amplify only the modified RNA templates and solution hybridizationassays using heterologous nucleic acid-specific probes. In addition, insitu hybridization and immunocytochemistry according to standardprotocols can be done using heterologous nucleic acid specificpolynucleotide probes and antibodies, respectively, to localize sites ofexpression within transgenic tissue.

The present invention will be further described by reference to thefollowing detailed examples.

It is understood, however, that there are many extensions, variations,and modifications on the basic theme of the present invention beyondthat shown in the examples and description, which are within the spiritand scope of the present invention. All publications, patents, andpatent applications cited herein are hereby incorporated by reference.

EXAMPLES Example 1 Replicating Vectors and Recombination

Vector construction was done using standard molecular biologytechniques. T-DNA vectors were constructed to test whether recombinantT-DNA molecules could be produced and could persist in transformed maizecells using a viral replication mechanism acting in concert withrecombination. The recombination event could be site-specific,homologous or illegitimate recombination. The basic vector designcomprised at least one source of microhomology that could be used tocircularize the T-DNA. For example, overlapping areas of the neo gene,FRTI sites, or the left and right T-DNA borders can be used as theregions of microhomology. A recombination event within the neo gene,FRT1 sites, or the border sequences should generate replicationcompetent, circular T-DNAs which therefore leads to the activation of arecombination marker gene, for example neo which conferskanamycin-resistance, or gusA. In order to recover replicating T-DNAmolecules from E. coli, the ampicillin-resistance gene was incorporatedinto the T-DNA structure. A FLP recombinase gene, driven by a separatepromoter, can be provided on the same T-DNA or provided by anothervector.

A. The Effect of Replicase Expression on Homologous Recombination ofT-DNA

TABLE 1 Plasmid Description Neo Rep P10525RB-Ubipro/intron-GUS-Ubi-Bar-LB No No P16821LB-3′Δneo-Rep-WDVLIR-Ubipro/intron- Inactive Yes GUS-AMP-5′Δneo-RBP16822 RB-3′Δneo-Rep-WDVLIR-Ubipro/intron- Inactive YesGUS-AMP-5′Δneo-LB P16823 RB-3′Δneo-WDVLIR-Ubipro/intron- Inactive NoGUS-AMP-5′Δneo-LB P16824 RB-neo-Rep-WDVLIR-Ubipro/intron- Active Yes

Two truncated inactive neo genes on the same T-DNA were used to monitorthe homologous recombination between T-DNAs in BMS cells. One neo genehas a 5′ deletion (5′Δneo), while the second gene has a 3′ deletion(3′Δneo), both truncated fragments share a significant region ofoverlapping homology comprising 653 bp. Experiments were done in eitherthe presence or absence of WDV Replicase (Rep). If homologousrecombination occurs, inactive neo genes are restored to produce anactive, full-length neo gene and the cells acquire kanamycin-resistance.

BMS cells were transformed with the vectors of Table 1 according to theAgrobacterium-mediated transformation protocol illustrated in Example3A. Plasmid P10525 is a positive control transformation vector.Untransformed BMS cells were used as the negative control.

T-DNA recombinants were identified by the ability to transform E. coli.In order to test for recombinants, DNA was isolated from untransformedBMS cells (negative control) and transformed BMS cells. Further, todetermine if the T-DNAs could recombine in Agrobacterium, DNA wasisolated from the strains used for Agrobacterium-mediated transformationof BMS cells.

DNA was isolated from 2 ml aliquots of Agrobacterium 3 hours afteracetosyringone induction. Plasmid DNA was isolated using the Qiagen DNAmini-prep kit (Qiagen, Valencia, Calif.) according to the manufacturer'sinstructions. An aliquot of each sample was adjusted to a standardconcentration of 17 ng/μl and used for further analysis. All DNA sampleswere stored at −20° C.

DNA was extracted from BMS cells harvested 7 days after co-cultivationwith Agrobacterium using the DNeasy Plant Mini Kit (Qiagen, Valencia,Calif.) according to the manufacturer's instructions. Briefly, 100 mg ofBMS cells were ground to a fine powder in pre-chilled mortars and liquidnitrogen. 400 μl of extraction buffer (buffer AP1) and 4 μl of Rnase Astock (100 mg/ml) were added to the ground cells. Isolated DNA waseluted in either water or buffer AE. DNA concentration was estimatedusing the PicoGreen dsDNA quantitation kit (Molecular Probes, Eugene,Oreg.). An aliquot of each DNA sample was adjusted to 17 ng/μl. All DNAsamples were stored at −20° C.

Forty microliters of library-efficiency DH5α E. coli (GibcoBRL) wastransformed with 24 ng of DNA from each treatment by electroporation.The electroporation was performed in a Bio-Rad Gene Pulser (Bio-Rad,Hercules, Calif.) at 2.5 KV with capacitance set at 25 μF, resistanceset at 200 ohms and time set at constant using 2 mm cuvettes.Electroporated cells were incubated in 0.6 ml of 2×YT media at 37° C.for 30 min. After incubation, 0.2 ml samples were dispensed onto agarplates containing LB medium supplemented with 0.1 g/L ampicillin. Theplates were incubated overnight at 37° C., the number of colonies perplate was counted. The number of recovered colonies per plate wasaveraged for each treatment.

Forty colonies were randomly picked and inoculated onto LB agar platescontaining kanamycin (0.1 g/L) to screen for homologous recombinants.The results of this screen are shown in Table 2.

TABLE 2 Kanamycin resistance generated by homologous recombination ofT-DNA Ampicillin-resistant colonies Transformation Total Kan-Resistant %BMS only 0 0 0 Agro only 77  1/20 5 BMS + Agro 39  0/20 0 BMS + (Agro +Rep) 313 65/80 82Number of recovered, ampicillin- and kanamycin-resistant colonies afterE. coli electroporation with DNA isolated from BMS cells only,Agrobacterium only, or BMS cells co-cultivated with Agrobacterium.BMS+Agro: DNA from BMS cells co-cultivated with Agrobacterium containingT-DNA without the rep gene (P16823)BMS+(Agro+rep): DNA from BMS cells co-cultivated with Agrobacteriumcontaining T-DNA (P16821 or P16822) with the rep geneThe column labeled as “Total” presents the total number ofampicillin-resistant colonies recovered from each particular treatment.The column “Kan-Resistant” presents the fraction of kanamycin-resistantcolonies recovered among the tested ampicillin-resistant colonies.

These results indicate that homologous recombination did not occur inthe Agrobacterium harboring the T-DNA, it only occurred in thetransformed BMS cells. Further, these results indicate that homologousrecombination occurred only in the presence of replicase (Rep), when Repwas deleted, no kanamycin-resistant colonies were recovered. Once therep gene was provided, 82% of the ampicillin-resistant colonies werealso kanamycin-resistant.

In order to show that the homologous recombination occurred in the BMScells and was not an artifact from the later E. coli transformation,isolated putative recombinant T-DNAs were subjected to exonuclease IIItreatment and used to transform E. coli as described above. Theexonuclease degrades linear DNA while circular recombinants are notaffected. No difference in transformation efficiency was observedbetween untreated and exonuclease III-treated T-DNAs. These resultsindicate that homologous recombination occurred in the BMS cells and wasnot an artifact of E. coli transformation.

A restriction digest followed by electrophoretic separation was used toconfirm that the kanamycin-resistant lines contained a restoredfull-length neo gene. A SacII restriction site was located upstream ofthe neo gene and a SphI site was located downstream of the neo gene. Ifthe neo gene is restored via homologous recombination to a full-lengthgene, a SacII/SphI restriction digest yields a band of 1009 bp on anagarose gel. If the truncated neo gene has not been restored tofull-length by recombination, a SacII/SphI restriction digest yields aband of 847 bp on an agarose gel. Control plasmids and DNA from 13kanamycin-resistant and 2 kanamycin-sensitive lines were subjected toSacII/SphI restriction enzyme digestion and agarose gel separation.Results confirm that 11 of the 13 kanamycin-resistant lines had a bandat 1009 bp consistent with the restoration of a full-length neo gene byhomologous recombination in BMS cells, the other two kanamycin resistantlines showed two bands of slightly >1009 bp and ≦847 bp, likelyindicating an additional rearrangement of the recombined neo gene. Bothkanamycin-sensitive lines lacked the presence of the 1009 bp bandindicative of a full-length neo gene.

PCR analysis was also used to confirm that kanamycin-resistance was dueto the restoration of a full-length neo gene by homologousrecombination.

B. Functional Replicase is Required to Increase Homologous Recombination

The pWI-11 vector was the source of the wheat dwarf virus (WDV)initiator protein gene (rep) (Ugaki, M. et al. (1991) Nucl. Acids Res.19:371–377). An NcoI-SacII fragment of this vector containing the repcoding sequence and the short intergenic region (SIR) was subcloned intothe multiple cloning site of pUC19. The long intergenic region (LIR)regulatory element was amplified by PCR to produce a BamHI-NcoIfragment, which was subsequently ligated with the rep NcoI-SphI fragmentand cloned into the BamHI/SphI restriction sites of a gusA expressionvector. This three-fragment ligation produced an expression vectorcontaining gusA and rep, whose expression was controlled by thebi-directional (divergent) promoters within the LIR region. The LIRregion also contained the origin of replication (ori) required forvector amplification in plant cells. Subsequently, the gusA gene wasmodified to include the potato ST LS1 intron (Vancanneyt, G. et al.,(1990) Mol. Gen. Genet. 220:245–250). The maize ubi1 intron (Christensenand Quail (1996) Transgenic Res. 5:213–218) containing an FRT1 site wasinserted between the LIR promoter and the gusA coding sequence.

In order to produce T-DNA vectors, a synthetic FRT1 site (48 bp) wasinserted into the multiple cloning site between two T-DNA bordersequences in pSB11 (Ishida, Y. et al. (1996) Nat. Biotech. 14:745–750).The gusA/rep-containing vectors, which included the plasmid backbonewith the ampicillin-resistant gene, were integrated into this site byin-vitro site-specific recombination catalyzed by the FLP protein. Thereaction contained 25 mM Tris-HCl, pH 7.4, 1 mM EDTA, 1 mM DTT, 5%glycerol, 0.1 mM NaCl, 2 μg each of the FRT1-containing vectors to beintegrated, and 1.4 μg of FLP protein in a total volume of 10 μl.Incubation was for 60 min at 30° C. Two microliters of the incubationmixture were used for transformation of library efficiency DH5α E. colicompetent cells (Cat# 18263-012, Invitrogen, Carlsbad, Calif.) accordingto the manufacturer's specifications. Bacterial colonies were grown at37° C. overnight in spectinomycin-containing (100 mg/L) LB medium andthen transferred into 2 ml of ampicillin-containing (100 mg/L) liquid LBmedium for identification and DNA preparation ofdouble-antibiotic-resistant, co-integrative plasmids.

Five vectors were generated as shown in Table 3 below. In experimentalconstructs, the gusA gene is separated from its promoter by T-DNA bordersequences. Any recombination event within the FRT1 sites or the bordersequences will generate replication competent circular T-DNAs in whichthe recombination marker gene, gusA, is activated. SUG indicates anopposite orientation of the gusA gene in relation to its promoter on theother end of the T-DNA. Two promoters were used to drive the expressionof gusA, a maize ubiquitin promoter (Upro) was used in thetransformation control vectors (Upro-SUG and Upro-GUS), and v-sensepromoter (Wpro) of WDV was used in the experimental vectors (Wpro-SUG,W-proRep-SUG, and WproRepm-SUG). The v-sense promoter is part of the LIRcompact viral genetic element. This element also contains the viral(+)strand DNA replication origin (ori) and regulatory sequencescontrolling expression of the WDV initiator protein (Rep).

Tri-parental mating or electroporation was used to integrate thepSB11-based vectors into the super-binary vector pSB1 residing inAgrobacterium tumefaciens strain LBA 4404. Co-integrates were identifiedby double selection of transformed Agrobacterium colonies on mediacontaining spectinomycin and tetracyclin at 100 mg/L each. Restrictionanalysis was used to verify the structural integrity of the super-binaryvectors.

TABLE 3 GUS constructs Plasmid Description Rep WproRepm-SUGRB-FRT1/Ubi3′intron-3′gusA-Amp^(r)- No LIR/Repm-Ubi5′intron-FRT1-LBWproRep-SUG RB-FRT1/Ubi3′intron-3′gusA-Amp^(r)- YesLIR/Rep-Ubi5′intron-FRT1-LB Wpro-SUGRB-FRT1/Ubi3′intron-3′gusA-Amp^(r)-LIR- No Ubi5′intron-FRT1-LB Upro-SUGRB-FRT1/Ubi3′intron-3′gusA-Amp^(r)- No Ubipro-Ubi5′intron-FRT1-LB

TABLE 4 Recovery of T-DNAs Number of colonies/plate Plasmid 3 Days 6Days WproRepm-SUG 28 ± 4 10 ± 8  WproRep-SUG 25 ± 6 170 ± 20  Wpro-SUG13 ± 1 18 ± 4  Upro-GUS  1 ± 0 0.5 ± 0.7

BMS cells were transformed with the vectors of Table 3 as described inExample 3A. Circular, recombinant T-DNAs were recovered from total DNApreparations obtained from BMS cells three and six days aftertransformation (see Table 4) and used to transformation of DH5α E. colias described earlier. In the WproRep-SUG treatment, moreampicillin-resistant colonies were observed using DNA isolated from BMScells six days after transformation compared to DNA isolated three daysafter transformation. No such increase was seen in the Wpro-SUGtreatment, where the vector lacks the initiator protein (rep) gene, orin the WproRepm-SUG treatment, where the C2 open reading frame of theinitiator rep gene was mutated to eliminate replication function. Theseresults indicate that more recombinant T-DNA molecules are produced inBMS cells in the presence of the WDV replicase six days aftertransformation. Since the initiation of T-DNA recombination/replicationrequires accumulation of the rep gene product, the process is apparentlydelayed compared to a direct expression of transformation marker genesin transgenic BMS cells (see also Table 6).

TABLE 5 Recovery of T-DNAs +/− FLP Number of colonies/plate 3 Days 6Days Plasmid −FLP +FLP −FLP +FLP WproRep-SUG 25 ± 6 28 ± 6 170 ± 20 504± 107 Wpro-SUG 13 ± 1 20 ± 3  18 ± 4   20 ± 9 

The circular, recombinant T-DNAs can be formed by site-specificrecombination at the FRT1 sites, or by homologous recombination at theT-DNA borders. As analyzed by PCR, in the absence of FLP, junction sitesare generated mostly by the recombination around the border sequences,as indicated by a 661 bp PCR product resulting from border-to-borderrecombination. In the presence of FLP, the size of the predominant PCRproduct is smaller and corresponds to the expected size of theFRT-recombined T-DNA molecules of 307 bp. Generation of these moleculeswas independent of the method of FLP delivery, as the FLP expressionunit was provided on the same T-DNA, delivered by co-transformation, orby a combination of both methods. Further, in treatments with FLP, noPCR amplification signal was observed from the border-to-borderjunction.

Circular T-DNA molecules recovered 6 days after co-cultivation wereanalyzed further. No recombinant T-DNA molecules were recovered fromtreatments containing only FLP with no Rep. A random sample of 27recombinant T-DNAs was sequenced through the recombination sites toverify that they were generated by site-specific recombination. Of those27 T-DNAs sequenced, 20 T-DNA junction sites were the result ofrecombination events within the two FRT1 sites, presumably catalyzed byFLP.

TABLE 6 GUS expression GUS expression (nmol MU/min/PCV BMS cells) Daysafter Transformation Plasmid 1 2 3 4 5 6 7 No DNA 4 6 7 7 7 6 6WproRep-SUG 13 16 11 52 134 395 518 Upro-SUG 6 10 38 37 58 92 52Upro-GUS 8 78 179 242 275 278 277

The gusA gene separated from its promoter by T-DNA border sequencesproduced strong GUS activity in BMS cells co-cultivated with anAgrobacterium strain containing the WproRep-SUG T-DNA (see Table 6).Expression of GUS was delayed by about 1–2 days as compared to the fullyfunctional gusA expression cassette, Upro-GUS, which was used as apositive control. This delay could not be attributed to backgroundactivity since the Upro-SUG control showed only a fraction of the GUSactivity observed in the WproRep-SUG treatment. In addition, no GUSactivity was detectable when the ubiquitin promoter in Upro-GUS wasreplaced with the LIR promoter. The LIR promoter is only activated inthe presence of the initiator Rep protein. These results indicate afunctional gusA gene was generated by a concomitant recombination andreplication of T-DNAs.

A sample of recombinant T-DNA molecules recovered from treatments withthe Wpro-SUG vector was sequenced to determine the junction sites aroundthe left border. Among 44 randomly selected clones, 33 producedsequencing data. Among them, only two recombinant T-DNAs originated fromrecombination events at the same site, i.e. 2 of 33 events had the samejunction sequence. One recombination junction site was identified withinthe FRT sequences sharing a perfect 76 bp homology, but FLP protein wasnot provided in this particular treatment, therefore the recombinationwas based on sequence homology and not produced by the action of asite-specific recombinase. These results indicate the population ofrecombinant T-DNAs generated is likely highly heterogeneous and may notoriginate from a limited number of T-DNA recombination events.

Sequence analysis of the LB junction sites indicated a variety ofstructural features. While no precise right and left border T-DNAjunctions were identified, two intact RB ends and one LB ends were foundin conjunction with the other modified T-DNA ends. Microhomologiesranging from 1 to 6 bp were common at the crossover sites. Four examplesof filler DNA at the junction sites were found. The sequencing primerwas positioned about 350 bp from the left border, which biased theanalysis towards recovery of left border junction sequences.Nonetheless, 75% of randomly selected clones produced sequencing dataindicating that left border recombination was a preferred mode forgenerating recombinant T-DNAs.

Example 2 Vectors for Plant Transformation

Vector construction is done using standard molecular biology techniques.The method of transformation is not critical to the invention, thereforeany method of transformation can be used, and vector construction and/orinsert preparation can be modified accordingly.

A. Introduced Transgene and Targeting Vector

i. Introduced GUS Transgene

An Agrobacterium transformation vector was constructed containing a GUSexpression cassette between the left and right borders. The GUSexpression cassette comprised 5′UTR::Ubiquitin promoter::maize ubiquitinintron 1::gusA exon 1::gusA intron 1::gusA exon 2::pinIIterminator::3′UTR. The 5′ and 3′ regions each have one SphI site. SphIrestriction enzyme digestion produces a 6.0–6.5 kb DNA fragment. PCRprimers hybridizing to ubi intron 1 and gusA intron 2 amplify a 0.7 kbfragment. The overall structure of the transgene is as follows:

5′ ubi pro::ubi intron 1::gusA exon 1::gusA intron 1::gusA exon 2::pinII3′

ii. GUS Targetinq Vector

The introduced gusA transgene was used as a target site for a genetargeting experiment. The gene targeting vector was contained betweenthe left and right border in an Agrobacterium transformation vector. Thegene targeting vector was designed to replace gusA exon 1 with a barselectable marker gene which contains a SphI site. Restriction digestionwith SphI now results in a 2.3 kb fragment. PCR amplification with theprimers directed to introns 1 and 2 generates a 1.1 kb fragment. Removalof the gusA exon 1 eliminates GUS expression.

The structure of the gene targeting vector is as follows:

5′LB-ubi pro::ubi intron 1::bar:gusA intron 2::gusA exon2-LIR::Rep::SIR-RB 3′ wherein LIR is the Wheat Dwarf Virus (WDV) longintergenic region containing the promoter and origin of replication; Repis the WDV replicase gene; and SIR is the WDV short intergenic regioncontaining polyadenylation signals.B. Gene Targeting System for an Endogenous Genomic Target Site:Acetohydroxy-acid Synthase (AHAS)

Point mutations in acetohydroxy-acid synthase (AHAS) can be introducedto confer either a sulfonylurea or imidazolinone herbicide resistancephenotype in plants.

i. Tobacco

There are two genetically unlinked AHAS loci, SuRA and SuRB, inNicotiana tabacum, herbicide resistance can be mediated by mutation ateither locus (Chaleff et al. (1986) in Molecular Strategies for CropProtection: UCLA Symposium on Molecular and Cellular Biology,48:415–425, Arntzen and Ryan Eds, John Wiley and Sons, NY; Lee et al.(1988) EMBO J. 7:1241–1248). For example, a sulfonylurea herbicideresistance phenotype can be generated in tobacco by targetedmodification of SuRB to convert Trp 573-Leu 573 (W573L) as described byLee et al. (1990) Plant Cell 2:415–425. The targeting vectors used inLee et al. (supra) can be modified to enhance gene targeting frequencyby the inclusion of an origin of replication (ori) and a replicaseexpression cassette. Using standard vector construction and molecularbiology techniques, gene targeting vector pAGS182BV is modified asfollows:

3′RB-5′ΔAHAS-3′ocs::nptII::pnos-3′ocs::Rep::pnos-ori—LB 5′ wherein5′ΔAHAS indicates a 5′ deleted version of the SurB gene containing theW573L mutation as described by Lee et al. (supra). The resulting vectorwill be referenced as pAGS182Bvrep. Vector pAGS180BV can be modified ina similar way.

ii. Maize

Two AHAS genes, AHAS108 and AHAS109, have been reported in maize (Fanget al. (1992) Plant Mol. Biol. 18:1185–1187), herbicide resistance canbe generated by mutation at either locus. For example, a sulfonylureaherbicide resistance phenotype can be generated in maize by a targetedmodification of AHAS108 to convert Pro 165-Ala 165 (P165A) as describedby Lee et al. (1988) EMBO J. 7:1241–1248. An imidazolinone herbicideresistance phenotype can be generated in maize by a targetedmodification of AHAS108 to convert Ser 621-Asn 621 (S621 N) as describedby Sathasivan et al. (1991) Plant Physiol. 97:1044–1050.

Using standard vector construction and molecular biology techniques,targeting vectors can be constructed as follows:

5′ LB-ori-ubi::Rep::nos—AHAS108 S621 N-RB 3′

5′LB-ori-ubi::Rep::nos—AHAS108 P165A-RB 3′

The mutant AHAS genes are not operably linked to a promoter, thereforerandom integration is unlikely to yield a herbicide resistant phenotype.

C. Targeting Vectors Introduced by Sexual Crosses

In order to be maintained for delivery via sexual crosses, the targetingvector must be integrated into the genome of a plant and excised aftercrossing to a second plant. Therefore the targeting vector must beflanked by excision sequences, for example site-specific recombinationsites or transposon terminal repeats. This example outlines a strategyusing a site-specific recombinase.

The targeting vector is flanked at the 5′ and 3′ ends by directlyrepeated FRT sequences. Adjacent to the 5′ FRT (i.e. directly inside theFRT site) is the Wheat Dwarf Virus replicase gene (the Rep C1:C2sequence). Adjacent to the 3′ FRT site (i.e. directly inside the site)is a promoter, for example the Wheat Dwarf Virus LIR which contains theviral promoter elements and the viral origin of replication (ori). Inthe center of the cassette (i.e. in between the LIR and the replicasegene) is the mutant AHAS sequence (i.e. the target-modifying sequence).This arrangement is shown below:

5′FRT-replicase-mutant AHAS-LIR (Promoter & ori)-FRT 3′ Outside thetargeting vector, but within the T-borders, is a selection cassette, forexample UBI::bar::pinII. The transformation cassette is shown below:

5′ LB-ubi::bar::pinII-FRT-replicase-mutant AHAS-LIR-FRT 3′

Example 3 Transformation

This example provides methods of plant transformation and regenerationusing the polynucleotides of the present invention. The method oftransformation is not critical to the invention, therefore any method oftransformation can be used.

A. Agrobacterium-Mediated Transformation of BMS Cells

Zea mays Black Mexican Sweet (BMS) cells were propagated in Murashigeand Skoog medium containing 4.3 g/L MS salts, 3% sucrose, 2 mg/L 2,4-D,0.1 g/L myoinositol, 0.5 mg/L nicotinic acid, 0.1 mg/L thiamine-HCL, 0.5mg/L pyridoxine-HCL, and 2 mg/L glycine, pH 5.6. The suspension cultureswere shaken at 125 rpm at 25° C. in the dark. For transformation,aliquots of cell suspension (5 ml, 0.4 packed cell volume/ml) weretransferred into 50-ml conical tubes and the MS medium was replaced with5 ml of N6 medium (4 g/L N6 basal salts, 6.85% sucrose, 1.5 mg/L 2,4-D,0.69 g/L L-proline, 0.5 mg/L thiamine-HCl, and 1× Eriksson's vitaminmix, pH 5.2) supplemented with acetosyringone at 0.1 mM concentration.The same medium (5 ml) was used to re-suspend the pellet of 2.5×10⁸Agrobacterium cells (centrifuged at 4K rpm for 15 min) that were grownovernight in 30 ml of a minimal medium containing 10.5 g/L K₂HPO₄, 4.5g/L KH₂PO₄, 1 g/L ammonium sulfate, 0.5 g/L sodium citrate dihydrate, 1mM magnesium sulfate, and 0.2% sucrose. The two cell suspensions, BMScells and Agrobacterium, were combined and placed on a gyratory shakerat 140 rpm for 3 hrs at 27° C. in the dark. Fifty μl samples of theBMS/Agrobacterium co-cultivation mixtures were placed on dry glassmicrofiber filters (VWR Scientific Products), and transferred onto theN6 co-cultivation medium similar to the one used for the initialpre-incubations but containing 3% sucrose, 2 mg/L 2,4-D, pH 5.8, andsupplemented with 0.3% agar. Plates were incubated in the dark at 27° C.for 24 hrs. Filters were transferred onto the same media supplementedwith 100 mg/L carbenicilin to eliminate Agrobacterium.

B. Particle Bombardment Transformation and Regeneration of Maize Callus

Immature maize embryos from greenhouse or field grown High type II donorplants are bombarded with a plasmid or insert containing polynucleotideof the invention. If the polynucleotide does not include a selectablemarker, another plasmid containing a selectable marker gene can beco-precipitated on the particles used for bombardment. For example, aplasmid containing the PAT gene (Wohlleben et al. (1988) Gene 70:25–37)which confers resistance to the herbicide Bialaphos can be used.Transformation is performed as follows.

The ears are surface sterilized in 50% Chlorox bleach plus 0.5% Microdetergent for 20 minutes, and rinsed two times with sterile water. Theimmature embryos are excised and placed embryo axis side down (scutellumside up), 25 embryos per plate. These are cultured on 560L agar medium 4days prior to bombardment in the dark. Medium 560L is an N6-based mediumcontaining Eriksson's vitamins, thiamine, sucrose, 2,4-D, and silvernitrate. The day of bombardment, the embryos are transferred to 560Ymedium for 4 hours and are arranged within the 2.5-cm target zone.Medium 560Y is a high osmoticum medium (560L with high sucroseconcentration).

The plasmid or insert DNA for transformation is precipitated onto 1.1 μm(average diameter) tungsten pellets using a CaCl₂ precipitationprocedure as follows: 100 μl prepared tungsten particles (0.6 mg) inwater, 20 μl (2 μg) DNA in TrisEDTA buffer (1 μg total), 100 μl 2.5 MCaC1₂, 40 μl 0.1 M spermidine.

Each reagent is added sequentially to the tungsten particle suspension.The final mixture is sonicated briefly. After the precipitation period,the tubes are centrifuged briefly, liquid removed, washed with 500 ml100% ethanol, and centrifuged again for 30 seconds. Again the liquid isremoved, and 60 μl 100% ethanol is added to the final tungsten particlepellet. For particle gun bombardment, the tungsten/DNA particles arebriefly sonicated and 5 μl spotted onto the center of each macrocarrierand allowed to dry about 2 minutes before bombardment.

The sample plates are bombarded at a distance of 8 cm from the stoppingscreen to the tissue, using a DuPont biolistics helium particle gun. Allsamples receive a single shot at 650 PSI, with a total of ten aliquotstaken from each tube of prepared particles/DNA.

Four to 12 hours post bombardment, the embryos are moved to 560P (a lowosmoticum callus initiation medium similar to 560L but with lower silvernitrate), for 3–7 days, then transferred to 560R selection medium, an N6based medium similar to 560P containing 3 mg/liter Bialaphos, andsubcultured every 2 weeks. After approximately 10 weeks of selection,callus clones are sampled for PCR and activity of the polynucleotide ofinterest. Positive lines are transferred to 288J medium, an MS-basedmedium with lower sucrose and hormone levels, to initiate plantregeneration. Following somatic embryo maturation (2–4 weeks),well-developed somatic embryos are transferred to medium for germinationand transferred to the lighted culture room. Approximately 7–10 dayslater, developing plantlets are transferred to medium in tubes for 7–10days until plantlets are well established.

Plants are then transferred to inserts in flats (equivalent to 2.5″ pot)containing potting soil and grown for 1 week in a growth chamber,subsequently grown an additional 1–2 weeks in the greenhouse, thentransferred to Classic™ 600 pots (1.6 gallon) and grown to maturity.Plants are monitored for expression of the polynucleotide of interest.

C. Agrobacterium -mediated Transformation and Regeneration of MaizeCallus

For Agrobacterium -mediated transformation of maize, a gene targetingvector of the present invention is introduced using the method of Zhao(U.S. Pat. No. 5,981,840, and PCT patent publication WO98/32326; thecontents of which are hereby incorporated by reference).

Briefly, immature embryos are isolated from maize and the embryoscontacted with a suspension of Agrobacterium containing a polynucleotideof the present invention, where the bacteria are capable of transferringthe nucleotide sequence of interest to at least one cell of at least oneof the immature embryos (step 1: the infection step). In this step theimmature embryos are immersed in an Agrobacterium suspension for theinitiation of inoculation. The embryos are co-cultured with theAgrobacterium (step 2: the co-cultivation step). The immature embryosare cultured on solid medium following the infection step. Followingthis co-cultivation period an optional “resting” step is available. Inthis resting step, the embryos are incubated in the presence of at leastone antibiotic known to inhibit the growth of Agrobacterium without theaddition of a selective agent for plant transformants (step 3: restingstep). The immature embryos are cultured on solid medium withantibiotic, but without a selecting agent, for elimination ofAgrobacterium and for a resting phase for the infected cells. Next,inoculated embryos are cultured on medium containing a selective agentand growing transformed callus is recovered (step 4: the selectionstep). The immature embryos are cultured on solid medium with aselective agent resulting in the selective growth of transformed cells.The callus is then regenerated into plants (step 5: the regenerationstep), and calli grown on selective medium are cultured on solid mediumto regenerate the plants.

D. Transformation of Dicots

A polynucleotide of the present invention can be introduced intoembryogenic suspension cultures of soybean by particle bombardment usingthe methods as essentially described in Parrott, W. A., L. M. Hoffman,D. F. Hildebrand, E. G. Williams, and G. B. Collins (1989) Plant CellRep. 7:615–617. This method, with modifications, is described below.

Seed is removed from pods when the cotyledons are between 3 and 5 mm inlength. The seeds are sterilized in a bleach solution (0.5%) for 15minutes after which time the seeds are rinsed with sterile distilledwater. The immature cotyledons are excised by first cutting away theportion of the seed that contains the embryo axis. The cotyledons arethen removed from the seed coat by gently pushing the distal end of theseed with the blunt end of the scalpel blade. The cotyledons are thenplaced (flat side up) SB1 initiation medium (MS salts, B5 vitamins, 20mg/L 2,4-D, 31.5 g/l sucrose, 8 g/L TC Agar, pH 5.8). The petri platesare incubated in the light (16 hr day; 75–80 μE) at 26° C. After 4 weeksof incubation the cotyledons are transferred to fresh SB1 medium. Afteran additional two weeks, globular stage somatic embryos that exhibitproliferative areas are excised and transferred to FN Lite liquid medium(Samoylov, V. M., D. M. Tucker, and W. A. Parrott (1998) In Vitro CellDev. Biol.—Plant 34:8–13). About 10 to 12 small clusters of somaticembryos are placed in 250 ml flasks containing 35 ml of SB172 medium.The soybean embryogenic suspension cultures are maintained in 35 mLliquid media on a rotary shaker, 150 rpm, at 26° C. with florescentlights (20 μE) on a 16:8 hour day/night schedule. Cultures aresub-cultured every two weeks by inoculating approximately 35 mg oftissue into 35 mL of liquid medium.

Soybean embryogenic suspension cultures are then transformed usingparticle gun bombardment (Klein et al. (1987) Nature (London) 327:70;U.S. Pat. No. 4,945,050). A BioRad Biolistic™ PDS1000/HE instrument canbe used for these transformations. A selectable marker gene, which isused to facilitate soybean transformation, is a chimeric gene composedof the 35S promoter from Cauliflower Mosaic Virus (Odell et al. (1985)Nature 313:810–812), the hygromycin phosphotransferase gene from plasmidpJR225 (from E. coli; Gritz et al. (1983) Gene 25:179–188) and the 3′region of the nopaline synthase gene from the T-DNA of the Ti plasmid ofAgrobacterium tumefaciens.

To 50 μL of a 60 mg/mL 1 μm gold particle suspension is added (inorder): 5 μL DNA (1 μg/μL), 20 μl spermidine (0.1 M), and 50 μL CaCl₂(2.5 M). The particle preparation is agitated for three minutes, spun ina microfuge for 10 seconds and the supernatant removed. The DNA-coatedparticles are washed once in 400 μL 70% ethanol and resuspended in 40 μLof anhydrous ethanol. The DNA/particle suspension is sonicated threetimes for one second each. Five μL of the DNA-coated gold particles isthen loaded on each macro carrier disk.

Approximately 300–400 mg of a two-week-old suspension culture is placedin an empty 60×15 mm petri dish and the residual liquid removed from thetissue with a pipette. Membrane rupture pressure is set at 1100 psi andthe chamber is evacuated to a vacuum of 28 inches mercury. The tissue isplaced approximately 8 cm away from the retaining screen, and isbombarded three times. Following bombardment, the tissue is divided inhalf and placed back into 35 ml of FN Lite medium.

Five to seven days after bombardment, the liquid medium is exchangedwith fresh medium. Eleven days post bombardment the medium is exchangedwith fresh medium containing 50 mg/mL hygromycin. This selective mediumis refreshed weekly. Seven to eight weeks post bombardment, green,transformed tissue will be observed growing from untransformed, necroticembryogenic clusters. Isolated green tissue is removed and inoculatedinto individual flasks to generate new, clonally propagated, transformedembryogenic suspension cultures. Each new line is treated as anindependent transformation event. These suspensions are then subculturedand maintained as clusters of immature embryos, or tissue is regeneratedinto whole plants by maturation and germination of individual embryos.

E. DNA Isolatio

i. DNA Isolation from Callus and Leaf Tissues

In order to screen putative transformation events for the presence ofthe transgene, genomic DNA is extracted from calluses or leaves using amodification of the CTAB (cetyltriethylammonium bromide, Sigma H5882)method described by Stacey and Isaac (1994). Approximately 100–200 mg offrozen tissues is ground into powder in liquid nitrogen and homogenizedin 1 ml of CTAB extraction buffer (2% CTAB, 0.02 M EDTA, 0.1 M Tris-HCIpH 8, 1.4 M NaCl, 25 mM DTT) for 30 min at 65° C. Homogenized samplesare allowed to cool at room temperature for 15 min before a singleprotein extraction with approximately 1 ml 24:1 v/v chloroform:octanolis done. Samples are centrifuged for 7 min at 13,000 rpm and the upperlayer of supernatant collected using wide-mouthed pipette tips. DNA isprecipitated from the supernatant by incubation in 95% ethanol on icefor 1 h. DNA threads are spooled onto a glass hook, washed in 75%ethanol containing 0.2 M sodium acetate for 10 min, air-dried for 5 minand resuspended in TE buffer. Five μl RNAse A is added to the samplesand incubated at 37° C. for 1 h.

For quantification of genomic DNA, gel electrophoresis is performedusing a 0.8% agarose gel in 1×TBE buffer. One microliter of the samplesare fractionated alongside 200, 400, 600 and 800 ng μl⁻¹ λ uncut DNAmarkers.

Example 4 Gene Targeting

This example provides methods and constructs used to produce a targetedmodification to a polynucleotide integrated in the host genome. Theexample describes the targeting of a stably introduced transgene, aswell as the targeting of an endogenous gene.

A. Targeted Modification of a Transgene

BMS cells were stably transformed with a gusA expression vector asdescribed in Example 3A. The gusA transgene is described in Example 2A,part i. The 5′ and 3′ regions of the transgene each have one SphI sitewhich result in a 6.0–6.5 kb fragment upon SphI restriction enzymedigestion. PCR primers hybridizing to intron 1 and intron 2 amplify a0.7 kb DNA fragment. GUS expression can be measured by several standardmethods known in the art, such as a quantitative fluorimetric assay asdescribed in (Jefferson et al. (1987) EMBO J. 6:3901–3907).

The introduced gusA transgene was used as a target for modification. Atargeting vector was designed which replaces gusA exon 1 with a barselectable marker gene containing a SphI site. Restriction digestionwith SphI now results in a 2.3 kb DNA fragment. PCR amplification withthe primers directed to introns 1 and 2 generates a 1.1 kb band. Removalof the gusA exon 1 eliminates GUS expression. The gusA target modifyingpolynucleotide shared a total of about 2 kb homology with the gusAtarget.

Calli transformed with the gusA targeting vector were sequentiallyscreened as follows: bar⁺ calli were selected on Basta. These bar⁺ callirepresent all transformation events. Basta-resistant calli were furtherscreened for GUS activity using a fluorimetric assay to identifyputative gene targeting events (see Table 7 below). Random integrationevents should be bar⁺, GUS⁺ while gene targeting events should be bar⁺,GUS⁻. Some GUS⁻ events could be generated by gene silencing, thereforeputative gene targeting events, along with controls were furtheranalyzed by PCR with primers directed to introns 1 and 2. The loss ofthe 0.7 kb band is diagnostic of a gene targeting event. Cells withrandomly integrated targeting vector were GUS⁺, bar⁺, with PCR productsof 1.1 kb and 0.7 kb. Cells comprising a gene targeted modification wereGUS⁻, bar⁺, with a PCR product of 1.1 kb only, for example events CD4and CF5. Selected events were further evaluated by Southern analysis ofgenomic DNA digested with SphI using a gusA exon 2 probe confirmed theabsence of a ˜6.0–6.5 kb band and the presence of a 2.3 kb band in genetargeting events. While not all putative events were fullycharacterized, of 364 Basta-resistant calli generated 2 gene targetingevents were fully confirmed using the process described above.Therefore, the frequency of gene targeting is at least 5.5×10⁻³, whichcorresponds well with observations in Arabidopsis (Puchta et al. (1996)PNAS 93:5055–5060).

TABLE 7 Gene targeted knockout of GUS expression GUS expression (nmolMU/min/PCV BMS cells) Time (min) Cell Line 0 15 28 51 83 108 136 BMScontrol 14 21 22 38 43 43 40 FLG75 27 272 511 873 1374 1856 2202 CD4 1828 61 91 119 134 124 CF5 28 42 68 88 116 148 158 AC4 23 64 191 302 428561 678 BMS control = Untransformed BMS cells used as negative controlFLG75 = gusA target line used as positive control CD4 = gene targetingevent, confirmed by PCR CF5 = gene targeting event, confirmed by PCR AC4= random integrant, gene silencingB. Targeted Modification of an Endogenous Gene

Point mutations in acetohydroxy-acid synthase (AHAS) can be introducedto confer either a sulfonylurea or imidazolinone herbicide resistancephenotype in plants. The following examples describe the targetedmodification of tobacco and maize genes to confer herbicide resistance.

i. Tobacco

Transformation, selection, and characterization of AHAS gene targetingevents can be done as described in Lee et al. (1990) Plant Cell2:415–425 using the modified vector pAGS182BVrep described in Example2B, as well as the original control and targeting vectors used. Genetargeting frequency can be measured by comparing the frequency oftargeted modification with vector pAGS182BVrep to the frequency withvector pAGS182BV.

ii. Maize

Transformation with AHAS targeting vectors of Example 2B can be done asdescribed in Example 3C. Selection, and characterization of AHAS genetargeting events can be done as described in Zhu et al. (1999) PNAS96:8768–8773. Gene targeting events should exhibit herbicide resistancewhile random integration events should be herbicide sensitive. Genetargeting frequency can be measured by comparing the frequency oftargeted modification with the vectors of Example 2B to the frequencywith control vectors lacking either the origin of replication or thefunctional replicase expression cassette.

Example 5 Crossing-Mediated Gene Targeting

This example provides methods of gene targeting by sexually crossingindividual plants. Crossing plants results in gene targeting events inthe developing embryos. The endogenous acetohydroxy-acid synthase (AHAS;E.C. 4.1.3.18), a key enzyme in the synthesis of the branched chainamino acids, is targeted to be converted to a mutated form that impartsresistance to an imidazolinone herbicide.

In this example, two transgenic plant lines are developed. The firsttransgenic line comprises a FLP recombinase expression cassette, and theendogenous AHAS gene. The second transgenic line comprises an integratedAHAS gene targeting vector flanked by FRT-sites. By crossing these twolines, the targeting vector is excised by FLP recombinase wherein it cangenerate AHAS gene targeted modification resulting in an imidazolinoneherbicide resistance phenotype in the progeny.

A. Recombinase Transgenic Lines

The FLP-expression cassette is introduced into a maize plant comprisingthe endogenous AHAS gene, to produce a transgenic event. This constructcontains a selection cassette (UBI::bar::pinII) and a cassette forconstitutive-expression of a recombinase (UBI::moFLP::pinII) both withinan Agrobacterium binary vector. This cassette is transformed into amaize inbred (for example the Pioneer inbred PHN46) using Agrobacterium-mediated transformation as described in Example 3C, and Bialaphosselection is used to recover transgenic events. Transgenic events areassessed for single-copy integration using Southern analysis, andfurther analyzed for FLP activity (see for example WO 99/25841).Single-copy, FLP-active events are regenerated, the plants grown tomaturity, and selfed or outcrossed to produce transgenic seed.

B. Targeting Vector Transgenic Lines

The second construct is also an Agrobacterium transformation vector.Inside the T-borders of this construct are the molecular componentsnecessary for crossing-base homologous recombination, the targetingvector. The targeting vector is described in Example 2C.

The targeting vector is transformed into immature embryos from the PHN46inbred, and Bialaphos selection is used to recover transgenic events.The Bialaphos-resistant transformants are screened for single-copyintegration and these events are regenerated. The resulting plants areselfed or outcrossed to produce transgenic seed.

C. Crossing and Target Modification

Using stable transformants from the two transgenic lines, crosses aremade between the events produced with the above two constructs. Thesecrosses can be made using TO transgenic plants, or with any progenygeneration of plants (T1, T2 . . . Tn). For example, T1 seed from bothtransformants is planted and grown to maturity. Upon crossing, the FLPrecombinase activity provided by the first transgenic line results inexcision of the FRT-flanked targeting vector from the copy of the genomethat came from the second transgenic line. When the FRT sites recombineto circularize the cassette, the LIR promoter sequence is juxtaposed tothe replicase gene, resulting in replicase expression. The circularizedtargeting vector replicates, enhancing homologous recombination betweenthe mutant-AHAS and the endogenous AHAS sequence. The result of thishomologous recombination is the targeted modification of the endogenousAHAS sequence to the mutant form which confers resistance toimidazolinone herbicides.

Progeny plants containing such as modified AHAS locus are screened bygerminating seedlings on 0.7 μM imazethapyr (AC263, 499, or Pursuit,technical grade, American Cyanamid), upon which herbicide-resistantplants are easily distinguished from wild-type plants (i.e. with anunaltered AHAS gene). Using this method, it is expected that themutant-AHAS herbicide-resistance phenotype will be conferred (viahomologous recombination) at much higher frequencies in the resultingprogeny (relative to a non-replicating control targeting vector).

D. Variations

Variations on this crossing-based strategy can also be incorporated.Examples include using inducible and/or developmental or tissue-specificpromoters to control expression of either the recombinase or thereplicase genes, using larger regions of homology (i.e. between thetarget sequence and the target-modifying sequence in the two respectiveplants to be crossed), or controlling replicase activity by usingvariants selected for decreased efficacy. Replication can also becontrolled by using single replicase component-genes from geminivirusesin which replicase functions have evolved in separate genes (forexample, using the AL1 gene from the AL1, AL2, AL3 replicase complex inTomato Golden Mosaic Virus, see Hanley-Bowdoin et al. (1990) PNAS (USA)87(4):1446–1450).

In another variation, one transgenic line can be produced whichcomprises the integrated targeting vector and a recombinase expressioncassette under control of an inducible promoter. This transgenic linecan be crossed to a non-transgenic line, and recombinase expressioninduced such that the progeny of the cross comprise gene targetedmodifications in a non-transgenic background. Using the gene target ofthe current example, AHAS, these progeny could be easily screened.

In other variations the targeting vector is flanked by the terminalelements of transposons. In these cases, a transposase is provided toexcise the targeting vector.

The above examples are provided to illustrate the invention but not tolimit its scope. Other variants of the invention will be readilyapparent to one of ordinary skill in the art and are encompassed by theappended claims. All publications, patents, patent applications, andcomputer programs cited herein are hereby incorporated by reference.

1. A method for gene targeting in a plant cell comprising: (a) providingthe plant cell, wherein the plant cell comprises a targetpolynucleotide, wherein the target polynucleotide is endogenous to theplant cell; (b) introducing into the plant cell a targeting vectorcomprising a target modifying polynucleotide and a geminiviral origin ofreplication, wherein the target modifying polynucleotide has at least75–150 bp of homology to the target polynucleotide, wherein thetargeting vector is integrated into the plant genome, and wherein thetargeting vector is flanked by site-specific recombination sites forexcision; (c) providing a site-specific recombinase to excise thetargeting vector, wherein the excised targeting vector forms a nucleicacid molecule capable of replication; (d) providing an appropriate viralreplicase, wherein the replicase binds to the geminiviral origin ofreplication, to stimulate homologous recombination between the targetmodifying polynucleotide and the target polynucleotide to produce amodified target polynucleotide; and (e) recovering the plant cellcomprising the modified target polynucleotide integrated into itsgenome.
 2. The method of claim 1 wherein the replicase is provided byexpression of a gene on an expression cassette.
 3. The method of claim 1wherein the targeting vector further comprises a replicase-encodingpolynucleotide operably linked to a promoter.
 4. The method of claim 3wherein the replicase-encoding polynucleotide is operably linked to aconstitutive promoter.
 5. The method of claim 1 wherein the plant cellis from a monocot or a dicot.
 6. The method of claim 5 wherein the plantcell is selected from the group consisting of maize, rice, wheat, oats,barley, sorghum, millet, soybean, canola, Brassica, alfalfa, sunflower,safflower, Arabidopsis, cotton, and tobacco.
 7. The method of claim 1further comprising generating a plant comprising the modified targetpolynucleotide.
 8. A method for gene targeting in a plant comprising:(a) sexually crossing a donor plant and a target plant, wherein thetarget plant comprises integrated into its genome a targeting vectorcomprising a target modifying polynucleotide and a geminiviral origin ofreplication, wherein the targeting vector is flanked by site-specificrecombination sites, wherein the target modifying polynucleotide has atleast 75–150 bp of homology to the target polynucleotide and is capableof homologous recombination with an endogenous genomic targetpolynucleotide in the target plant, wherein the target plant furthercomprises an appropriate viral replicase which binds to the origin ofreplication, wherein the donor plant comprises a site-specificrecombinase; (b) growing the target plant for a time sufficient toproduce seed having a modified target polynucleotide integrated into itsgenome; and (c) recovering the seed having the modified targetpolynucleotide integrated into its genome.
 9. The method of claim 8wherein the plant is a monocot or a dicot.
 10. The method of claim 9wherein the plant is selected from the group consisting of maize, rice,wheat, oats, barley, sorghum, millet, soybean, canola, Brassica,alfalfa, sunflower, safflower, Arabidopsis, cotton, and tobacco.
 11. Themethod of claim 1, wherein the geminivirus is a wheat dwarf virus. 12.The method of claim 1, wherein the site-specific recombinase is a FLPrecombinase.
 13. The method of claim 1, wherein the site-specificrecombination sites for excision are FRT sites.
 14. The method of claim13, wherein the FRT sites are FRT1.
 15. The method of claim 8, whereinthe geminivirus is a wheat dwarf virus.
 16. The method of claim 8,wherein the site-specific recombinase is a FLP recombinase.
 17. Themethod of claim 8, wherein the site-specific recombination sites forexcision are FRT sites.
 18. The method of claim 17, wherein the FRTsites are FRT1.